add CLAUDE.md with project context for Claude Code (#261)

* add CLAUDE.md with project context for Claude Code

Provides development commands, architecture overview, file conventions,
custom S3 classes, data files, testing setup, and versioning guidelines
to help Claude Code assist effectively in this repository.

https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx

* add CLAUDE.md to .Rbuildignore

Excludes the Claude Code context file from the R package build tarball.

https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx

* document version-bump requirement for every PR in CLAUDE.md

Each PR must increment the .9zzz dev counter by 1 in both
DESCRIPTION (Version: field) and NEWS.md (top-level heading).

https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx

---------

Co-authored-by: Claude <noreply@anthropic.com>

.Rbuildignore

@@ -9,6 +9,7 @@
 ^_pkgdown\.yml$
 ^appveyor\.yml$
 ^codecov\.yml$
+^CLAUDE\.md$
 ^cran-comments\.md$
 ^CRAN-RELEASE$
 ^\.github$
@@ -40,3 +41,4 @@
 ^CRAN-SUBMISSION$
 ^PythonPackage$
 ^README\.Rmd$
+\.no_include$

.github/ISSUE_TEMPLATE/1-bug-report.yml

@@ -42,7 +42,7 @@ body:
       multiple: false
       options:
         - ''
-        - Latest CRAN version (3.0.0)
-        - One of the latest GitHub versions (3.0.0.9xxx)
+        - Latest CRAN version (3.0.1)
+        - One of the latest GitHub versions (3.0.1.9xxx)
     validations:
       required: true

.github/prehooks/pre-commit

@@ -48,7 +48,6 @@ echo "Running prehook..."
 if command -v Rscript > /dev/null; then
   if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
     Rscript -e "source('data-raw/_pre_commit_checks.R')"
-    currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
     echo "- Adding changed files in ./data-raw and ./man to this commit"
     git add data-raw/*
     git add data/*
@@ -57,11 +56,9 @@ if command -v Rscript > /dev/null; then
     git add NAMESPACE
   else
     echo "- R package 'pkgload', 'devtools', or 'dplyr' not installed!"
-    currentpkg="your"
   fi
 else
   echo "- R is not available on your system!"
-  currentpkg="your"
 fi
 echo ""
 
@@ -92,7 +89,7 @@ else
   
   # Combine tag and commit number
   currentversion="$currenttag.$((currentcommit + 9001))"
-  echo "- ${currentpkg} pkg version set to ${currentversion}"
+  echo "- AMR pkg version set to ${currentversion}"
   
   # Update version number and date in DESCRIPTION
   sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
@@ -103,10 +100,7 @@ else
   
   # Update version number in NEWS.md
   if [ -e "NEWS.md" ]; then
-    if [ "$currentpkg" = "your" ]; then
-      currentpkg=""
-    fi
-    sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
+    sed -i -- "1s/.*/# AMR ${currentversion}/" NEWS.md
     echo "- Updated version number in ./NEWS.md"
     rm -f NEWS.md--
     git add NEWS.md

.github/workflows/check-current-testthat-dev-versions.yaml

@@ -18,7 +18,7 @@
 # This R package is free software; you can freely use and distribute   #
 # it for both personal and commercial purposes under the terms of the  #
 # GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# the Free Software Foundation.
+# the Free Software Foundation.                                        #
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
@@ -28,18 +28,37 @@
 # ==================================================================== #
 
 on:
+  pull_request:
+    # run in each PR in this repo
+    branches: '**'
   push:
     branches: '**'
-  pull_request:
-    branches: '**'
+  schedule:
+    # also run a schedule everyday at 1 AM.
+    # this is to check that all dependencies are still available (see R/zzz.R)
+    - cron:  '0 1 * * *'
 
-name: lintr
+name: check-recent-dev-pkgs
 
 jobs:
-  lintr:
-    runs-on: ubuntu-latest
+  R-code-check:
+    runs-on: ${{ matrix.config.os }}
+
+    continue-on-error: ${{ matrix.config.allowfail }}
+
+    name: ${{ matrix.config.os }} (dev-pkgs)
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # current 'release' version on Ubuntu
+          - {os: ubuntu-latest,  r: 'release', allowfail: false}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
     steps:
       - uses: actions/checkout@v4
 
@@ -47,39 +66,21 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: release
-          # use RStudio Package Manager to quickly install packages
-          use-public-rspm: true
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: false
+          extra-repositories: >
+            https://tidyverse.r-universe.dev
+            https://r-lib.r-universe.dev
+            https://tidymodels.r-universe.dev
+            https://yihui.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::lintr
-            any::cyclocomp
-            any::roxygen2
-            any::devtools
-            any::usethis
+          extra-packages: any::rcmdcheck
+          needs: check
+          upgrade: 'TRUE'
 
-      - name: Remove unneeded folders
-        run: |
-          # do not check these folders
-          rm -rf data-raw
-          rm -rf tests
-          rm -rf vignettes
-          
-      - name: Lint
-        run: |
-          # get ALL linters, not just default ones
-          linters <- getNamespaceExports(asNamespace("lintr"))
-          linters <- sort(linters[grepl("_linter$", linters)])
-          # lose deprecated
-          linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator|consecutive_stopifnot|no_tab|single_quotes|unnecessary_nested_if|unneeded_concatenation)_linter$", linters)]
-          linters <- linters[linters != "linter"]
-          # and the ones we find unnnecessary
-          linters <- linters[!grepl("^(commented_code|extraction_operator|implicit_integer|indentation|line_length|namespace|nonportable_path|object_length|object_name|object_usage|is)_linter$", linters)]
-          # put the functions in a list
-          linters_list <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
-          names(linters_list) <- linters
-          # run them all!
-          lintr::lint_package(linters = linters_list, exclusions = list("R/aa_helper_pm_functions.R"))
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/check-old-tinytest.yaml

@@ -50,11 +50,11 @@ jobs:
           # For these old versions, dependencies and vignettes will not be checked.
           # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases).
           - {os: ubuntu-latest, r: '3.6', allowfail: false}
-          # - {os: windows-latest, r: '3.5', allowfail: true} # always fails, horrible with UTF-8
-          - {os: ubuntu-latest, r: '3.4', allowfail: false}
-          - {os: ubuntu-latest, r: '3.3', allowfail: false}
-          - {os: ubuntu-latest, r: '3.2', allowfail: false}
-          - {os: ubuntu-latest, r: '3.1', allowfail: false}
+          # - {os: windows-latest, r: '3.5', allowfail: false} # always fails, horrible with UTF-8
+          # - {os: ubuntu-latest, r: '3.4', allowfail: false}  # 3.1-3.4 now always fails with Error in grep(warn_re, lines, invert = TRUE, value = TRUE) attempt to set index 46/46 in SET_STRING_ELT
+          # - {os: ubuntu-latest, r: '3.3', allowfail: false}
+          # - {os: ubuntu-latest, r: '3.2', allowfail: false}
+          # - {os: ubuntu-latest, r: '3.1', allowfail: false}
           - {os: ubuntu-latest, r: '3.0', allowfail: false}
 
     env:
@@ -76,9 +76,14 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install tinytest from CRAN
+      - name: Install suggested pkgs (and tinytest) from CRAN
         run: |
-          install.packages("tinytest", repos = "https://cran.r-project.org")
+          desc_lines <- readLines('DESCRIPTION')
+          suggests <- readLines('DESCRIPTION')[grepl("^(Suggests:|  )", readLines('DESCRIPTION'))]
+          suggests <- suggests[(which(grepl("^Suggests", suggests)) + 1):length(suggests)]
+          suggests <- gsub("[ ,]", "", suggests)
+          pkgs <- unique(c(suggests, "tinytest"))
+          for (p in pkgs) try(install.packages(p, repos = "https://cran.r-project.org"), silent = TRUE)
         shell: Rscript {0}
 
       - name: Show session info

.github/workflows/publish-to-pypi.yml

@@ -39,7 +39,7 @@ jobs:
     runs-on: ubuntu-latest
     
     env:
-      PYPI_PAT: ${{ secrets.PYPI_PAT }}
+      GH_REPO_SCOPE: ${{ secrets.GH_REPO_SCOPE }}
     
     steps:
       - name: Checkout code
@@ -78,6 +78,7 @@ jobs:
           cd PythonPackage/AMR
           python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*
 
+      # TODO - Support Miniconda and Anaconda too
       # - name: Set up Miniconda
       #   continue-on-error: true
       #   uses: conda-incubator/setup-miniconda@v2
@@ -117,7 +118,7 @@ jobs:
           rm -rf PythonPackage
 
           git init
-          git remote add origin https://$PYPI_PAT@github.com/msberends/AMR
+          git remote add origin https://$GH_REPO_SCOPE@github.com/msberends/AMR
           git checkout --orphan python-wrapper
           git config user.name "github-actions[bot]"
           git config user.email "github-actions[bot]@users.noreply.github.com"
@@ -125,4 +126,4 @@ jobs:
           git rm -rf . || true
           git add .
           git commit -m "Python wrapper update"
-          git push https://$PYPI_PAT@github.com/msberends/AMR.git python-wrapper --force
+          git push https://$GH_REPO_SCOPE@github.com/msberends/AMR.git python-wrapper --force

.github/workflows/renew-gpt-training-data.yml

@@ -39,7 +39,7 @@ jobs:
     runs-on: ubuntu-latest
     
     env:
-      PYPI_PAT: ${{ secrets.PYPI_PAT }}
+      GH_REPO_SCOPE: ${{ secrets.GH_REPO_SCOPE }}
     
     steps:
       - name: Checkout code
@@ -63,4 +63,4 @@ jobs:
           git config user.email "github-actions[bot]@users.noreply.github.com"
           git add latest_training_data.txt
           git commit -m "GPT training data update"
-          git push https://$PYPI_PAT@github.com/msberends/amr-for-r-assistant.git main --force
+          git push https://$GH_REPO_SCOPE@github.com/msberends/amr-for-r-assistant.git main --force

.github/workflows/todo-tracker.yml

@@ -0,0 +1,84 @@
+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
+# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
+# Journal of Statistical Software, 104(3), 1-31.                       #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://amr-for-r.org              #
+# ==================================================================== #
+
+on:
+  push:
+    # only on main
+    branches: "main"
+
+name: Update TODO Tracker
+
+jobs:
+  update-todo:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Generate TODO list from R/
+        run: |
+          export TZ=Europe/Amsterdam
+          last_updated=$(date +"%e %B %Y %H:%M:%S %Z" | sed 's/^ *//')
+          echo "## \`TODO\` Report" > todo.md
+          echo "" >> todo.md
+          echo "**Last Updated: ${last_updated}**" >> todo.md
+          echo "" >> todo.md
+          echo "_This overview is automatically updated on each push to \`main\`. It provides an automated overview of all mentions of the text \`TODO\`._" >> todo.md
+          echo "" >> todo.md
+          todos=$(grep -rn --include=\*.{R,Rmd,yaml,yml,md,css,js}  --exclude={todo-tracker.yml,todo.md} "TODO" . || true)
+          if [ -z "$todos" ]; then
+            echo "✅ No TODOs found." >> todo.md
+          else
+            echo "$todos" | awk -F: -v repo="https://github.com/msberends/AMR/blob/main/" '
+              {
+                file = $1
+                gsub("^\\./", "", file)  # remove leading ./ if present
+                line = $2
+                text = substr($0, index($0,$3))
+                if (file != last_file) {
+                  if (last_file != "") print "```"
+                  print ""
+                  print "### [`" file "`](" repo file ")"
+                  print "```r"
+                  last_file = file
+                }
+                printf "L%s: %s\n", line, text
+              }
+            ' >> todo.md
+            echo "\`\`\`" >> todo.md
+          fi
+
+      - name: Update GitHub issue
+        uses: peter-evans/create-or-update-comment@v4
+        with:
+          token: ${{ secrets.GH_REPO_SCOPE }}
+          issue-number: 231
+          comment-id: 3253439219
+          body-file: todo.md
+          edit-mode: replace

.github/workflows/website.yaml

@@ -42,16 +42,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      - uses: actions/checkout@v4
+      - name: checkout
+        uses: actions/checkout@v4
         with:
           # this is to keep timestamps, the default fetch-depth: 1 gets the timestamps of the moment of cloning
           # we need this for the download page on our website - dates must be of the files, not of the latest git push
           fetch-depth: 0
 
-      - name: Preserve timestamps
-        run: |
-          sudo apt install git-restore-mtime
-          git restore-mtime
+      - name: restore timestamps
+        uses: chetan/git-restore-mtime-action@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.gitignore

@@ -1,5 +1,6 @@
 Meta
 doc
+docs
 .Renviron
 .Rproj.user
 .Rhistory

CLAUDE.md

@@ -0,0 +1,167 @@
+# CLAUDE.md — AMR R Package
+
+This file provides context for Claude Code when working in this repository.
+
+## Project Overview
+
+**AMR** is a zero-dependency R package for antimicrobial resistance (AMR) data analysis using a One Health approach. It is peer-reviewed, used in 175+ countries, and supports 28 languages.
+
+Key capabilities:
+- SIR (Susceptible/Intermediate/Resistant) classification using EUCAST 2011–2025 and CLSI 2011–2025 breakpoints
+- Antibiogram generation: traditional, combined, syndromic, and WISCA
+- Microorganism taxonomy database (~79,000 species)
+- Antimicrobial drug database (~620 drugs)
+- Multi-drug resistant organism (MDRO) classification
+- First-isolate identification
+- Minimum Inhibitory Concentration (MIC) and disk diffusion handling
+- Multilingual output (28 languages)
+
+## Common Commands
+
+All commands run inside an R session:
+
+```r
+# Rebuild documentation (roxygen2 → .Rd files + NAMESPACE)
+devtools::document()
+
+# Run all tests
+devtools::test()
+
+# Full package check (CRAN-level: docs + tests + checks)
+devtools::check()
+
+# Build pkgdown website locally
+pkgdown::build_site()
+
+# Code coverage report
+covr::package_coverage()
+```
+
+From the shell:
+
+```bash
+# CRAN check from parent directory
+R CMD check AMR
+```
+
+## Repository Structure
+
+```
+R/              # All R source files (62 files, ~28,000 lines)
+man/            # Auto-generated .Rd documentation (do not edit manually)
+tests/testthat/ # testthat test files (test-*.R) and helper-functions.R
+data/           # Pre-compiled .rda datasets
+data-raw/       # Scripts used to generate data/ files
+vignettes/      # Rmd vignette articles
+inst/           # Installed files (translations, etc.)
+_pkgdown.yml    # pkgdown website configuration
+```
+
+## R Source File Conventions
+
+**Naming conventions in `R/`:**
+
+| Prefix/Name | Purpose |
+|---|---|
+| `aa_*.R` | Loaded first (helpers, globals, options, package docs) |
+| `zz_deprecated.R` | Deprecated function wrappers |
+| `zzz.R` | `.onLoad` / `.onAttach` initialization |
+
+**Key source files:**
+
+- `aa_helper_functions.R` / `aa_helper_pm_functions.R` — internal utility functions (large; ~63 KB and ~37 KB)
+- `aa_globals.R` — global constants and breakpoint lookup structures
+- `aa_options.R` — `amr_options()` / `get_AMR_option()` system
+- `mo.R` / `mo_property.R` — microorganism lookup and properties
+- `ab.R` / `ab_property.R` — antimicrobial drug functions
+- `av.R` / `av_property.R` — antiviral drug functions
+- `sir.R` / `sir_calc.R` / `sir_df.R` — SIR classification engine
+- `mic.R` / `disk.R` — MIC and disk diffusion classes
+- `antibiogram.R` — antibiogram generation (traditional, combined, syndromic, WISCA)
+- `first_isolate.R` — first-isolate identification algorithms
+- `mdro.R` — MDRO classification (EUCAST, CLSI, CDC, custom guidelines)
+- `amr_selectors.R` — tidyselect helpers for selecting AMR columns
+- `interpretive_rules.R` / `custom_eucast_rules.R` — clinical interpretation rules
+- `translate.R` — 28-language translation system
+- `ggplot_sir.R` / `ggplot_pca.R` / `plotting.R` — visualisation functions
+
+## Custom S3 Classes
+
+The package defines five S3 classes with full print/format/plot/vctrs support:
+
+| Class | Created by | Represents |
+|---|---|---|
+| `<mo>` | `as.mo()` | Microorganism code |
+| `<ab>` | `as.ab()` | Antimicrobial drug code |
+| `<av>` | `as.av()` | Antiviral drug code |
+| `<sir>` | `as.sir()` | SIR value (S/I/R/SDD) |
+| `<mic>` | `as.mic()` | Minimum inhibitory concentration |
+| `<disk>` | `as.disk()` | Disk diffusion diameter |
+
+## Data Files
+
+Pre-compiled in `data/` (do not edit directly; regenerate via `data-raw/` scripts):
+
+| File | Contents |
+|---|---|
+| `microorganisms.rda` | ~79,000 microbial species with full taxonomy |
+| `antimicrobials.rda` | ~620 antimicrobial drugs with ATC codes |
+| `antivirals.rda` | Antiviral drugs |
+| `clinical_breakpoints.rda` | EUCAST + CLSI breakpoints (2011–2025) |
+| `intrinsic_resistant.rda` | Intrinsic resistance patterns |
+| `example_isolates.rda` | Example AMR dataset for documentation/testing |
+| `WHONET.rda` | Example WHONET-format dataset |
+
+## Zero-Dependency Design
+
+The package has **no `Imports`** in `DESCRIPTION`. All optional integrations (ggplot2, dplyr, data.table, tidymodels, cli, crayon, etc.) are listed in `Suggests` and guarded with:
+
+```r
+if (requireNamespace("pkg", quietly = TRUE)) { ... }
+```
+
+Never add packages to `Imports`. If new functionality requires an external package, add it to `Suggests` and guard usage appropriately.
+
+## Testing
+
+- **Framework:** `testthat` (R ≥ 3.1); legacy `tinytest` used for R 3.0–3.6 CI
+- **Test files:** `tests/testthat/test-*.R`
+- **Helpers:** `tests/testthat/helper-functions.R`
+- **CI matrix:** GitHub Actions across Windows / macOS / Linux × R devel / release / oldrel-1 through oldrel-4
+- **Coverage:** `covr` (some files excluded: `atc_online.R`, `mo_source.R`, `translate.R`, `resistance_predict.R`, `zz_deprecated.R`, helper files, `zzz.R`)
+
+## Documentation
+
+- All exported functions use **roxygen2** blocks (`RoxygenNote: 7.3.3`, markdown enabled)
+- Run `devtools::document()` after any change to roxygen comments
+- Never edit files in `man/` directly — they are auto-generated
+- Vignettes live in `vignettes/` as `.Rmd` files
+- The pkgdown website is configured in `_pkgdown.yml`
+
+## Versioning
+
+Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)
+
+- Development versions use a `.9xxx` suffix
+- Stable CRAN releases drop the dev suffix (e.g., `3.0.1`)
+- `NEWS.md` uses sections **New**, **Fixes**, **Updates** with GitHub issue references (`#NNN`)
+
+### Version bump required for every PR
+
+Before opening a pull request, always increment the four-digit dev counter by 1 in **both** of these files:
+
+1. **`DESCRIPTION`** — the `Version:` field:
+   ```
+   Version: 3.0.1.9021  →  Version: 3.0.1.9022
+   ```
+
+2. **`NEWS.md`** — the top-level heading:
+   ```
+   # AMR 3.0.1.9021  →  # AMR 3.0.1.9022
+   ```
+
+Read the current version from `DESCRIPTION`, add 1 to the last numeric component, and write the new version to both files in the same commit as the rest of the PR changes.
+
+## Internal State
+
+The package uses a private `AMR_env` environment (created in `aa_globals.R`) for caching expensive lookups (e.g., microorganism matching scores, breakpoint tables). This avoids re-computation within a session.

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 3.0.0
-Date: 2025-06-01 16:52:53 UTC
-SHA: 79038fed2169a25a7fc067c80bb25d9d78be21d9
+Version: 3.0.1
+Date: 2025-09-20 10:56:46 UTC
+SHA: 33fb1849eb5aa6d33828e643c8f5047dd93447e3

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.0.9017
-Date: 2025-07-28
+Version: 3.0.1.9021
+Date: 2026-02-12
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by
@@ -27,10 +27,10 @@ Authors@R: c(
   person(given = c("Judith", "M."),                 family = "Fonville",    role = "ctb"),
   person(given = c("Kathryn"),                      family = "Holt",        role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
   person(given = c("Larisse"),                      family = "Bolton",      role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
-  person(given = c("Matthew"),                      family = "Saab",        role = "ctb"),
+  person(given = c("Matthew"),                      family = "Saab",        role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
   person(given = c("Natacha"),                      family = "Couto",       role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
   person(given = c("Peter"),                        family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
-  person(given = c("Rogier", "P."),                 family = "Schade",      role = "ctb"),
+  person(given = c("Rogier", "P."),                 family = "Schade",      role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
   person(given = c("Sofia"),                        family = "Ny",          role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
   person(given = c("Alex", "W."),                   family = "Friedrich",   role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
   person(given = c("Bhanu", "N.", "M."),            family = "Sinha",       role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
@@ -70,5 +70,5 @@ BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE, old_usage = TRUE)

NAMESPACE

@@ -161,6 +161,8 @@ export(administrable_per_os)
 export(age)
 export(age_groups)
 export(all_antimicrobials)
+export(all_disk)
+export(all_disk_predictors)
 export(all_mic)
 export(all_mic_predictors)
 export(all_sir)
@@ -212,6 +214,7 @@ export(cephalosporins_4th)
 export(cephalosporins_5th)
 export(clear_custom_antimicrobials)
 export(clear_custom_microorganisms)
+export(clsi_rules)
 export(count_I)
 export(count_IR)
 export(count_R)
@@ -242,6 +245,7 @@ export(ggplot_sir_predict)
 export(glycopeptides)
 export(guess_ab_col)
 export(inner_join_microorganisms)
+export(interpretive_rules)
 export(is.ab)
 export(is.av)
 export(is.disk)
@@ -319,6 +323,7 @@ export(oxazolidinones)
 export(pca)
 export(penicillins)
 export(phenicols)
+export(phosphonics)
 export(polymyxins)
 export(proportion_I)
 export(proportion_IR)
@@ -358,6 +363,7 @@ export(sir_df)
 export(sir_interpretation_history)
 export(sir_predict)
 export(skewness)
+export(spiropyrimidinetriones)
 export(step_mic_log2)
 export(step_sir_numeric)
 export(streptogramins)
@@ -381,6 +387,8 @@ if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, disk)
 if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, mic)
 if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, resistance_predict)
 if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, sir)
+if(getRversion() >= "3.0.0") S3method(ggplot2::scale_type, mic)
+if(getRversion() >= "3.0.0") S3method(ggplot2::scale_type, sir)
 if(getRversion() >= "3.0.0") S3method(knitr::knit_print, antibiogram)
 if(getRversion() >= "3.0.0") S3method(knitr::knit_print, formatted_bug_drug_combinations)
 if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, ab)
@@ -402,6 +410,7 @@ if(getRversion() >= "3.0.0") S3method(recipes::prep, step_mic_log2)
 if(getRversion() >= "3.0.0") S3method(recipes::prep, step_sir_numeric)
 if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_mic_log2)
 if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_sir_numeric)
+if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, ab)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mic)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)

NEWS.md

@@ -1,13 +1,52 @@
-# AMR 3.0.0.9017
-
-This is primarily a bugfix release, though we added one nice feature too.
+# AMR 3.0.1.9021
 
 ### New
-* Integration with the **tidymodels** framework to allow seamless use of MIC and SIR data in modelling pipelines via `recipes`
+* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
   - `step_mic_log2()` to transform `<mic>` columns with log2, and `step_sir_numeric()` to convert `<sir>` columns to numeric
-  - New `tidyselect` helpers: `all_mic()`, `all_mic_predictors()`, `all_sir()`, `all_sir_predictors()`
+  - New `tidyselect` helpers:
+    - `all_sir()`, `all_sir_predictors()`
+    - `all_mic()`, `all_mic_predictors()`
+    - `all_disk()`, `all_disk_predictors()`
+* Data set `esbl_isolates` to practise with AMR modelling
+* AMR selectors `phosphonics()` and `spiropyrimidinetriones()`
+* Support for Wildtype (WT) / Non-wildtype (NWT) in `as.sir()`, all plotting functions, and all susceptibility/resistance functions.
+  - `as.sir()` gained an argument `as_wt_nwt`, which defaults to `TRUE` only when `breakpoint_type = "ECOFF"` (#254)
+  - This transforms the output from S/R to WT/NWT
+  - Functions such as `susceptibility()` count WT as S and NWT as R
+* `interpretive_rules()`, which allows future implementation of CLSI interpretive rules (#235)
+  - `eucast_rules()` has become a wrapper around that function.
+
+### Fixes
+* Fixed a bug in `antibiogram()` for when no antimicrobials are set
+* Fixed a bug in `as.sir()` where for numeric input the arguments `S`,  `I`,  and `R` would not be considered (#244)
+* Fixed some foreign translations of antimicrobial drugs
+* Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
+* Fixed a bug to disregard `NI` for susceptibility proportion functions
+* Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256)
+
+### Updates
+* `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
+* `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255)
+* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
+* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)
+* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set
+* Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244)
+* Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243)
+  * Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"`
+  * Interpretation of capped MIC values now consistently returns `"NI"` (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode
+  * This results in more reliable behaviour compared to previous versions for capped MIC values
+  * Removed the `"inverse"` option, which has now become redundant
+* `ab_group()` now returns values consist with the AMR selectors (#246)
+
+
+# AMR 3.0.1
+
+This is a bugfix release following the release of v3.0.0 in June 2025.
 
 ### Changed
+* Fixed bugs introduced by `ggplot2` v4.0.0 (#236)
+  * MIC scale functions (such as `scale_y_mic()`) will now be applied automatically when plotting values of class `mic`
+  * SIR scale functions (such as `scale_x_sir()`) will now be applied automatically when plotting values of class `sir`
 * Fixed a bug in `antibiogram()` for when no antimicrobials are set
 * Fixed a bug in `antibiogram()` to allow column names containing the `+` character (#222)
 * Fixed a bug in `as.ab()` for antimicrobial codes with a number in it if they are preceded by a space
@@ -15,10 +54,19 @@ This is primarily a bugfix release, though we added one nice feature too.
 * Fixed a bug in `as.sir()` to allow any tidyselect language (#220)
 * Fixed a bug in `as.sir()` to pick right breakpoint when `uti = FALSE` (#216)
 * Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213)
+* Fixed a bug in `mdro()` to make sure all genes specified in arguments are acknowledged
+* Fixed a bug the `antimicrobials` data set to remove statins (#229)
+* Fixed a bug the `microorganisms` data set for MycoBank IDs and synonyms (#233)
+* Fixed ATC J01CR05 to map to piperacillin/tazobactam rather than piperacillin/sulbactam (#230)
+* Fixed skimmers (`skimr` package) of class `ab`, `sir`, and `disk` (#234)
 * Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (#223)
 * Fixed some specific Dutch translations for antimicrobials
+* Added a warning to `as.ab()` if input resembles antiviral codes or names (#232)
+* Added all reasons in verbose output of `mdro()` (#227)
 * Added `names` to `age_groups()` so that custom names can be given (#215)
 * Added note to `as.sir()` to make it explicit when higher-level taxonomic breakpoints are used (#218)
+* Added antibiotic codes from the Comprehensive Antibiotic Resistance Database (CARD) to the `antimicrobials` data set (#225)
+* Updated Fosfomycin to be of antibiotic class Phosphonics (#225)
 * Updated `random_mic()` and `random_disk()` to set skewedness of the distribution and allow multiple microorganisms
 
 

R/aa_globals.R

@@ -34,37 +34,37 @@ EUCAST_VERSION_BREAKPOINTS <- list(
     version_txt = "v15.0",
     year = 2025,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "14.0" = list(
     version_txt = "v14.0",
     year = 2024,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "13.1" = list(
     version_txt = "v13.1",
     year = 2023,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "12.0" = list(
     version_txt = "v12.0",
     year = 2022,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "11.0" = list(
     version_txt = "v11.0",
     year = 2021,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "10.0" = list(
     version_txt = "v10.0",
     year = 2020,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/"
+    url = "https://www.eucast.org/bacteria/document-archive/"
   )
 )
 EUCAST_VERSION_EXPERT_RULES <- list(
@@ -72,19 +72,19 @@ EUCAST_VERSION_EXPERT_RULES <- list(
     version_txt = "v3.3",
     year = 2021,
     title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
-    url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
+    url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
   ),
   "3.2" = list(
     version_txt = "v3.2",
     year = 2020,
     title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
-    url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
+    url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
   ),
   "3.1" = list(
     version_txt = "v3.1",
     year = 2016,
     title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
-    url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
+    url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
   )
 )
 EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
@@ -92,7 +92,7 @@ EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
     version_txt = "v1.2",
     year = 2023,
     title = "'EUCAST Expected Resistant Phenotypes'",
-    url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
+    url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
   )
 )
 
@@ -233,6 +233,7 @@ globalVariables(c(
   "uti_index",
   "value",
   "varname",
+  "where",
   "x",
   "xvar",
   "y",

R/aa_helper_functions.R

@@ -485,11 +485,7 @@ word_wrap <- function(...,
   }
 
   # format backticks
-  if (pkg_is_available("cli") &&
-    tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE) &&
-    tryCatch(getExportedValue("isAvailable", ns = asNamespace("rstudioapi"))(), error = function(e) {
-      return(FALSE)
-    }) &&
+  if (pkg_is_available("cli") && in_rstudio() &&
     tryCatch(getExportedValue("versionInfo", ns = asNamespace("rstudioapi"))()$version > "2023.6.0.0", error = function(e) {
       return(FALSE)
     })) {
@@ -502,11 +498,6 @@ word_wrap <- function(...,
       url = paste0("ide:help:AMR::", gsub("()", "", parts[cmds & parts %like% "[.]"], fixed = TRUE)),
       txt = parts[cmds & parts %like% "[.]"]
     )
-    # otherwise, give a 'click to run' popup
-    parts[cmds & parts %unlike% "[.]"] <- font_url(
-      url = paste0("ide:run:AMR::", parts[cmds & parts %unlike% "[.]"]),
-      txt = parts[cmds & parts %unlike% "[.]"]
-    )
     # datasets should give help page as well
     parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")] <- font_url(
       url = paste0("ide:help:AMR::", gsub("()", "", parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")], fixed = TRUE)),
@@ -689,8 +680,12 @@ format_included_data_number <- function(data) {
 vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
   # makes unique and sorts, and this also removed NAs
   v <- unique(v)
+  has_na <- anyNA(v)
   if (isTRUE(sort)) {
     v <- sort(v)
+    if (has_na) {
+      v <- c(v, NA)
+    }
   }
   if (isTRUE(reverse)) {
     v <- rev(v)
@@ -712,18 +707,25 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
     # class 'sir' should be sorted like this
     v <- c("S", "I", "R")
   }
-  if (identical(v, c("I", "NI", "R", "S", "SDD"))) {
+  if (identical(v, sort(VALID_SIR_LEVELS))) {
     # class 'sir' should be sorted like this
-    v <- c("S", "SDD", "I", "R", "NI")
+    v <- VALID_SIR_LEVELS
   }
   # oxford comma
   if (last_sep %in% c(" or ", " and ") && length(v) > 2) {
     last_sep <- paste0(",", last_sep)
   }
+  NAs <- which(is.na(v))
+
+  if (is.numeric(v)) {
+    v <- trimws(vapply(FUN.VALUE = character(1), v, format, scientific = FALSE))
+  }
+  quoted <- paste0(quotes, v, quotes)
+  quoted[NAs] <- "NA"
   # all commas except for last item, so will become '"val1", "val2", "val3" or "val4"'
   paste0(
-    paste0(quotes, v[seq_len(length(v) - 1)], quotes, collapse = ", "),
-    last_sep, paste0(quotes, v[length(v)], quotes)
+    paste(quoted[seq_len(length(quoted) - 1)], collapse = ", "),
+    last_sep, quoted[length(quoted)]
   )
 }
 
@@ -970,8 +972,13 @@ get_current_data <- function(arg_name, call) {
       # an element `.data` will be in the environment when using dplyr::select()
       return(env$`.data`)
     } else if (valid_df(env$training)) {
-      # an element `training` will be in the environment when using some tidymodels functions such as `prep()`
+      if (!is.null(env$x) && valid_df(env$x$template)) {
+        # an element `x$template` will be in the environment when using some tidymodels functions such as `prep()`
+        return(env$x$template)
+      } else {
+        # this is a fallback for some tidymodels functions such as `prep()`
         return(env$training)
+      }
     } else if (valid_df(env$data)) {
       # an element `data` will be in the environment when using older dplyr versions, or some tidymodels functions such as `fit()`
       return(env$data)
@@ -1041,24 +1048,8 @@ get_current_column <- function() {
 
   # cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
   frms <- lapply(sys.frames(), function(env) {
-    if (tryCatch(!is.null(env$i), error = function(e) FALSE)) {
-      if (!is.null(env$tibble_vars)) {
-        # for mutate_if()
-        # TODO remove later, was part of older dplyr versions (at least not in dplyr 1.1.4)
-        env$tibble_vars[env$i]
-      } else {
-        # for mutate(across())
-        if (!is.null(env$data) && is.data.frame(env$data)) {
-          df <- env$data
-        } else {
-          df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
-        }
-        if (is.data.frame(df)) {
-          colnames(df)[env$i]
-        } else {
-          env$i
-        }
-      }
+    if (all(c("dots", "i") %in% names(env))) {
+      names(env$dots)[env$i]
     } else {
       NULL
     }
@@ -1112,11 +1103,14 @@ format_custom_query_rule <- function(query, colours = has_colour()) {
   query <- gsub("any\\((.*)\\)$", paste0(font_black("any of "), "\\1"), query)
   query <- gsub("all\\((.*)\\)$", paste0(font_black("all of "), "\\1"), query)
   if (colours == TRUE) {
-    query <- gsub("[\"']R[\"']", font_rose_bg(" R "), query)
-    query <- gsub("[\"']SDD[\"']", font_orange_bg(" SDD "), query)
     query <- gsub("[\"']S[\"']", font_green_bg(" S "), query)
-    query <- gsub("[\"']NI[\"']", font_grey_bg(font_black(" NI ")), query)
+    query <- gsub("[\"']SDD[\"']", font_orange_bg(" SDD "), query)
     query <- gsub("[\"']I[\"']", font_orange_bg(" I "), query)
+    query <- gsub("[\"']R[\"']", font_rose_bg(" R "), query)
+    query <- gsub("[\"']NI[\"']", font_grey_bg(font_black(" NI ")), query)
+    query <- gsub("[\"']WT[\"']", font_green_bg(" SDD "), query)
+    query <- gsub("[\"']NWT[\"']", font_rose_bg(" I "), query)
+    query <- gsub("[\"']NS[\"']", font_rose_bg(" R "), query)
   }
   # replace the black colour 'stops' with blue colour 'starts'
   query <- gsub("\033[39m", "\033[34m", as.character(query), fixed = TRUE)
@@ -1188,6 +1182,13 @@ reset_all_thrown_messages <- function() {
   )
 }
 
+in_rstudio <- function() {
+  identical(Sys.getenv("RSTUDIO"), "1")
+}
+in_positron <- function() {
+  identical(Sys.getenv("POSITRON"), "1")
+}
+
 has_colour <- function() {
   if (is.null(AMR_env$supports_colour)) {
     if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") {
@@ -1222,7 +1223,7 @@ is_dark <- function() {
   AMR_env$current_theme <- tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) NULL)
   if (!identical(AMR_env$current_theme, AMR_env$former_theme) || is.null(AMR_env$is_dark_theme)) {
     AMR_env$former_theme <- AMR_env$current_theme
-    AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
+    AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) TRUE)
   }
   isTRUE(AMR_env$is_dark_theme)
 }
@@ -1617,8 +1618,8 @@ get_n_cores <- function(max_cores = Inf) {
 
 # Support `where()` if tidyselect not installed ----
 if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
-  # tidyselect::where() exists, load the namespace to make `where()`s work across the package in default arguments
-  loadNamespace("tidyselect")
+  # tidyselect::where() exists, retrieve from their namespace to make `where()`s work across the package in default arguments
+  where <- tidyselect::where
 } else {
   where <- function(fn) {
     # based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32

R/aa_options.R

@@ -29,15 +29,27 @@
 
 #' Options for the AMR package
 #'
-#' This is an overview of all the package-specific [options()] you can set in the `AMR` package.
-#' @section Options:
+#' @description
+#' This is an overview of all the package-specific options you can set in the `AMR` package. Set them using the [options()] function, e.g.:
+#'
+#' `options(AMR_guideline = "CLSI")`
+#' @section Options (alphabetical order):
 #' * `AMR_antibiogram_formatting_type` \cr A [numeric] (1-22) to use in [antibiogram()], to indicate which formatting type to use.
 #' * `AMR_breakpoint_type` \cr A [character] to use in [as.sir()], to indicate which breakpoint type to use. This must be either `r vector_or(clinical_breakpoints$type)`.
-#' * `AMR_capped_mic_handling` \cr A [character] to use in [as.sir()], to indicate how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted. Must be one of `"standard"`, `"strict"`, `"relaxed"`, or `"inverse"` - the default is `"standard"`.
+#' * `AMR_capped_mic_handling` \cr A [character] to use in [as.sir()], to indicate how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted. Must be one of `"none"`, `"conservative"`, `"standard"`, or `"lenient"` - the default is `"conservative"`.
 #' * `AMR_cleaning_regex` \cr A [regular expression][base::regex] (case-insensitive) to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to clean the user input. The default is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar".
 #' * `AMR_custom_ab` \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
 #' * `AMR_custom_mo` \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
 #' * `AMR_eucastrules` \cr A [character] to set the default types of rules for [eucast_rules()] function, must be one or more of: `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`.
+#' * `AMR_guideline` \cr A [character] to set the default guideline used throughout the `AMR` package wherever a `guideline` argument is available. This option is used as the default in e.g. [as.sir()], [resistance()], [susceptibility()], [interpretive_rules()] and many plotting functions. **While unset**, the AMR package uses the latest implemented EUCAST guideline (currently `r AMR::clinical_breakpoints$guideline[1]`).
+#'
+#'   - For [as.sir()], this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` to `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))` to `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`.
+#'
+#'   - For [resistance()] and [susceptibility()], this setting determines how the `"I"` (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, `"I"` is considered *resistant* in susceptibility calculations; under EUCAST, `"I"` is considered *susceptible* in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
+#'
+#'   - For [interpretive_rules()], this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.
+#'
+#'   - For many plotting functions (e.g., for MIC or disk diffusion values), supplying `mo` and `ab` enables automatic SIR-based interpretative colouring. These colours are derived from [as.sir()] in the background and therefore depend on the active `guideline` setting, which again uses `r AMR::clinical_breakpoints$guideline[1]` if not set explicitly.
 #' * `AMR_guideline` \cr A [character] to set the default guideline for interpreting MIC values and disk diffusion diameters with [as.sir()]. Can be only the guideline name (e.g., `"CLSI"`) or the name with a year (e.g. `"CLSI 2019"`). The default to the latest implemented EUCAST guideline, currently \code{"`r clinical_breakpoints$guideline[1]`"}. Supported guideline are currently EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
 #' * `AMR_ignore_pattern` \cr A [regular expression][base::regex] to ignore (i.e., make `NA`) any match given in [as.mo()] and all [`mo_*`][mo_property()] functions.
 #' * `AMR_include_PKPD` \cr A [logical] to use in [as.sir()], to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`.
@@ -63,9 +75,9 @@
 #'
 #' ...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with [as.sir()].
 #'
-#' ### Share Options Within Team
+#' ## Share Options Within Team
 #'
-#' For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
+#' For a more collaborative approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
 #'
 #' 1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
 #'

R/ab.R

@@ -54,7 +54,7 @@
 #' @section Source:
 #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 #'
-#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
+#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases ab
 #' @return A [character] [vector] with additional class [`ab`]
 #' @seealso
@@ -202,6 +202,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   if (sum(already_known) < length(x)) {
     progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
     on.exit(close(progress))
+    if (any(x_new[!already_known & !is.na(x_new)] %in% unlist(AMR_env$AV_lookup$generalised_all, use.names = FALSE), na.rm = TRUE)) {
+      warning_("in `as.ab()`: some input seems to resemble antiviral drugs - use `as.av()` or e.g. `av_name()` for these, not `as.ab()` or e.g. `ab_name()`.")
+    }
   }
 
   for (i in which(!already_known)) {
@@ -448,7 +451,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x_unknown <- x_unknown[!x_unknown %in% c("", NA)]
   if (length(x_unknown) > 0 && fast_mode == FALSE) {
     warning_(
-      "in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
+      "in `as.ab()`: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
       vector_and(x_unknown), "."
     )
   }
@@ -511,7 +514,7 @@ pillar_shaft.ab <- function(x, ...) {
   out[is.na(x)] <- font_na(NA)
 
   # add the names to the drugs as mouse-over!
-  if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
+  if (in_rstudio()) {
     out[!is.na(x)] <- font_url(
       url = paste0(x[!is.na(x)], ": ", ab_name(x[!is.na(x)])),
       txt = out[!is.na(x)]
@@ -627,6 +630,20 @@ rep.ab <- function(x, ...) {
   out
 }
 
+# this prevents the requirement for putting the dependency in Imports:
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, ab)
+get_skimmers.ab <- function(column) {
+  ab <- as.ab(column, info = FALSE)
+  ab <- ab[!is.na(ab)]
+  skimr::sfl(
+    skim_type = "ab",
+    n_unique = ~ length(unique(ab)),
+    top_ab = ~ names(sort(-table(ab)))[1L],
+    top_ab_name = ~ names(sort(-table(ab_name(ab, info = FALSE))))[1L],
+    top_group = ~ names(sort(-table(ab_group(ab, info = FALSE))))[1L]
+  )
+}
+
 generalise_antibiotic_name <- function(x) {
   x <- toupper(x)
   # remove suffices

R/ab_property.R

@@ -163,11 +163,29 @@ ab_tradenames <- function(x, ...) {
 }
 
 #' @rdname ab_property
+#' @param all_groups A [logical] to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting `all_groups = TRUE` would return all three for such an antibiotic, while `all_groups = FALSE` (default) only returns the most distinctive group name.
 #' @export
-ab_group <- function(x, language = get_AMR_locale(), ...) {
+ab_group <- function(x, language = get_AMR_locale(), all_groups = FALSE, ...) {
   meet_criteria(x, allow_NA = TRUE)
   language <- validate_language(language)
-  translate_into_language(ab_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
+  meet_criteria(all_groups, allow_class = "logical", has_length = 1)
+
+  grps <- ab_validate(x = x, property = "group", ...)
+  for (i in seq_along(grps)) {
+    if (all_groups == FALSE) {
+      # take the first match based on ABX_PRIORITY_LIST
+      grps[[i]] <- grps[[i]][1]
+    }
+    if (language != "en") {
+      grps[[i]] <- translate_into_language(grps[[i]], language = language, only_affect_ab_names = TRUE)
+    }
+  }
+  names(grps) <- x
+  if (length(grps) == 1 || all_groups == FALSE) {
+    unname(unlist(grps))
+  } else {
+    grps
+  }
 }
 
 #' @rdname ab_property
@@ -282,7 +300,7 @@ ab_info <- function(x, language = get_AMR_locale(), ...) {
     ab = as.character(x),
     cid = ab_cid(x),
     name = ab_name(x, language = language),
-    group = ab_group(x, language = language),
+    group = ab_group(x, language = language, all_groups = TRUE),
     atc = ab_atc(x),
     atc_group1 = ab_atc_group1(x, language = language),
     atc_group2 = ab_atc_group2(x, language = language),

R/amr_selectors.R

@@ -425,6 +425,14 @@ phenicols <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
   amr_select_exec("phenicols", only_sir_columns = only_sir_columns, return_all = return_all)
 }
 
+#' @rdname antimicrobial_selectors
+#' @export
+phosphonics <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(return_all, allow_class = "logical", has_length = 1)
+  amr_select_exec("phosphonics", only_sir_columns = only_sir_columns, return_all = return_all)
+}
+
 #' @rdname antimicrobial_selectors
 #' @export
 polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
@@ -450,6 +458,14 @@ rifamycins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
   amr_select_exec("rifamycins", only_sir_columns = only_sir_columns, return_all = return_all)
 }
 
+#' @rdname antimicrobial_selectors
+#' @export
+spiropyrimidinetriones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(return_all, allow_class = "logical", has_length = 1)
+  amr_select_exec("spiropyrimidinetriones", only_sir_columns = only_sir_columns, return_all = return_all)
+}
+
 #' @rdname antimicrobial_selectors
 #' @export
 streptogramins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
@@ -685,7 +701,7 @@ amr_select_exec <- function(function_name,
   }
 
   # untreatable drugs
-  untreatable <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$name %like% "(-high|EDTA|polysorbate|macromethod|screening|nacubactam)")]
+  untreatable <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$name %like% "(-high|EDTA|polysorbate|macromethod|screening|nacubactam|inducible)")]
   if (!is.null(vars_df) && only_treatable == TRUE) {
     if (any(untreatable %in% names(ab_in_data))) {
       if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
@@ -713,9 +729,9 @@ amr_select_exec <- function(function_name,
   if (is.null(amr_class_args) || isTRUE(function_name %in% c("antifungals", "antimycobacterials"))) {
     ab_group <- NULL
     if (isTRUE(function_name == "antifungals")) {
-      abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antifungals")]
+      abx <- AMR_env$AB_lookup$ab[which(vapply(FUN.VALUE = logical(1), AMR_env$AB_lookup$group, function(x) "Antifungals" %in% x))]
     } else if (isTRUE(function_name == "antimycobacterials")) {
-      abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antimycobacterials")]
+      abx <- AMR_env$AB_lookup$ab[which(vapply(FUN.VALUE = logical(1), AMR_env$AB_lookup$group, function(x) "Antimycobacterials" %in% x))]
     } else {
       # their upper case equivalent are vectors with class 'ab', created in data-raw/_pre_commit_checks.R
       # carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
@@ -723,7 +739,11 @@ amr_select_exec <- function(function_name,
       # manually added codes from add_custom_antimicrobials() must also be supported
       if (length(AMR_env$custom_ab_codes) > 0) {
         custom_ab <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% AMR_env$custom_ab_codes), ]
-        check_string <- paste0(custom_ab$group, custom_ab$atc_group1, custom_ab$atc_group2)
+        check_string <- paste0(
+          vapply(FUN.VALUE = character(1), custom_ab$group, function(x) paste(x, collapse = " ")),
+          custom_ab$atc_group1,
+          custom_ab$atc_group2
+        )
         if (function_name == "betalactams") {
           find_group <- "beta[-]?lactams"
         } else if (function_name %like% "cephalosporins_") {
@@ -819,10 +839,10 @@ c.amr_selector <- function(...) {
 
 all_any_amr_selector <- function(type, ..., na.rm = TRUE) {
   cols_ab <- c(...)
-  result <- cols_ab[toupper(cols_ab) %in% c("S", "SDD", "I", "R", "NI")]
+  result <- cols_ab[toupper(cols_ab) %in% VALID_SIR_LEVELS]
   if (length(result) == 0) {
     message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "S", "I" or "R"')
-    result <- c("S", "SDD", "I", "R", "NI")
+    result <- VALID_SIR_LEVELS
   }
   cols_ab <- cols_ab[!cols_ab %in% result]
   df <- get_current_data(arg_name = NA, call = -3)
@@ -931,7 +951,7 @@ any.amr_selector_any_all <- function(..., na.rm = FALSE) {
     }
   }
   # this is `!=`, so turn around the values
-  sir <- c("S", "SDD", "I", "R", "NI")
+  sir <- VALID_SIR_LEVELS
   e2 <- sir[sir != e2]
   structure(all_any_amr_selector(type = type, e1, e2),
     class = c("amr_selector_any_all", "logical")
@@ -1001,11 +1021,11 @@ find_ab_names <- function(ab_group, n = 3) {
   # try popular first, they have DDDs
   drugs <- AMR_env$AB_lookup[which((!is.na(AMR_env$AB_lookup$iv_ddd) | !is.na(AMR_env$AB_lookup$oral_ddd)) &
     AMR_env$AB_lookup$name %unlike% " " &
-    AMR_env$AB_lookup$group %like% ab_group &
+    vapply(FUN.VALUE = character(1), AMR_env$AB_lookup$group, function(x) paste(x, collapse = " ")) %like% ab_group &
     AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name
   if (length(drugs) < n) {
     # now try it all
-    drugs <- AMR_env$AB_lookup[which((AMR_env$AB_lookup$group %like% ab_group |
+    drugs <- AMR_env$AB_lookup[which((vapply(FUN.VALUE = character(1), AMR_env$AB_lookup$group, function(x) paste(x, collapse = " ")) %like% ab_group |
       AMR_env$AB_lookup$atc_group1 %like% ab_group |
       AMR_env$AB_lookup$atc_group2 %like% ab_group) &
       AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name

R/antibiogram.R

@@ -453,7 +453,7 @@ antibiogram.default <- function(x,
     deprecation_warning("antibiotics", "antimicrobials", fn = "antibiogram", is_argument = TRUE)
     antimicrobials <- list(...)$antibiotics
   }
-  meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer"), allow_NA = FALSE, allow_NULL = FALSE)
+  meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer", "function"), allow_NA = FALSE, allow_NULL = FALSE)
   if (!is.function(mo_transform)) {
     meet_criteria(mo_transform, allow_class = "character", has_length = 1, is_in = c("name", "shortname", "gramstain", colnames(AMR::microorganisms)), allow_NULL = TRUE, allow_NA = TRUE)
   }
@@ -518,6 +518,10 @@ antibiogram.default <- function(x,
 
   # get antimicrobials
   ab_trycatch <- tryCatch(colnames(suppressWarnings(x[, antimicrobials, drop = FALSE])), error = function(e) NULL)
+  if (is.null(ab_trycatch)) {
+    # try with tidyverse
+    ab_trycatch <- tryCatch(colnames(dplyr::select(x, {{ antimicrobials }})), error = function(e) NULL)
+  }
   if (is.null(ab_trycatch)) {
     stop_ifnot(is.character(suppressMessages(antimicrobials)), "`antimicrobials` must be an antimicrobial selector, or a character vector.")
     antimicrobials.bak <- antimicrobials
@@ -556,12 +560,11 @@ antibiogram.default <- function(x,
         next
       } else {
         # determine whether this new column should contain S, I, R, or NA
+        S_values <- c("S", "WT")
         if (isTRUE(combine_SI)) {
-          S_values <- c("S", "SDD", "I")
-        } else {
-          S_values <- "S"
+          S_values <- c(S_values, "SDD", "I")
         }
-        other_values <- setdiff(c("S", "SDD", "I", "R"), S_values)
+        other_values <- setdiff(c("S", "SDD", "I", "R", "WT", "NWT", "NS"), S_values)
         x_transposed <- as.list(as.data.frame(t(x[, abx, drop = FALSE]), stringsAsFactors = FALSE))
         if (isTRUE(only_all_tested)) {
           x[new_colname] <- as.sir(vapply(FUN.VALUE = character(1), x_transposed, function(x) ifelse(anyNA(x), NA_character_, ifelse(any(x %in% S_values), "S", "R")), USE.NAMES = FALSE))
@@ -580,7 +583,7 @@ antibiogram.default <- function(x,
     if (length(existing_ab_combined_cols) > 0 && !is.null(ab_transform)) {
       ab_transform <- NULL
       warning_(
-        "Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial agent columns (e.g., \"AMP+GEN\").\n\n",
+        "Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
         "To avoid incorrectly guessing which antimicrobials this represents, `ab_transform` was automatically set to `NULL`.\n\n",
         "If this is unintended, please rename the column(s) to avoid using '+' in the name, or set `ab_transform = NULL` explicitly to suppress this message."
       )
@@ -611,10 +614,9 @@ antibiogram.default <- function(x,
 
   counts <- out
 
+  out$n_susceptible <- out$S + out$WT
   if (isTRUE(combine_SI)) {
-    out$n_susceptible <- out$S + out$I + out$SDD
-  } else {
-    out$n_susceptible <- out$S
+    out$n_susceptible <- out$n_susceptible + out$I + out$SDD
   }
   if (all(out$n_tested < minimum, na.rm = TRUE) && wisca == FALSE) {
     warning_("All combinations had less than `minimum = ", minimum, "` results, returning an empty antibiogram")

R/atc_online.R

@@ -99,7 +99,8 @@ atc_online_property <- function(atc_code,
   read_html <- import_fn("read_html", "xml2")
 
   if (!all(atc_code %in% unlist(AMR::antimicrobials$atc))) {
-    atc_code <- as.character(ab_atc(atc_code, only_first = TRUE))
+    missing <- atc_code %unlike% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"
+    atc_code[missing] <- as.character(ab_atc(atc_code[missing], only_first = TRUE))
   }
 
   if (!has_internet()) {

R/av.R

@@ -51,7 +51,7 @@
 #' @section Source:
 #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 #'
-#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
+#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases av
 #' @return A [character] [vector] with additional class [`ab`]
 #' @seealso

R/bug_drug_combinations.R

@@ -43,7 +43,7 @@
 #' @details The function [format()] calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. [knitr::kable()].
 #' @export
 #' @rdname bug_drug_combinations
-#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "SDD", "I", "R", and "total".
+#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "SDD", "I", "R", "WT, "NWT", and "total".
 #' @examples
 #' # example_isolates is a data set available in the AMR package.
 #' # run ?example_isolates for more info.
@@ -111,6 +111,8 @@ bug_drug_combinations <- function(x,
       SDD = integer(0),
       I = integer(0),
       R = integer(0),
+      WT = integer(0),
+      NWT = integer(0),
       total = integer(0),
       total_rows = integer(0),
       stringsAsFactors = FALSE
@@ -133,6 +135,9 @@ bug_drug_combinations <- function(x,
           I = m["I", ],
           R = m["R", ],
           NI = m["NI", ],
+          WT = m["WT", ],
+          NWT = m["NWT", ],
+          NS = m["NS", ],
           na = m[which(is.na(rownames(m))), ],
           stringsAsFactors = FALSE
         )
@@ -146,8 +151,11 @@ bug_drug_combinations <- function(x,
         I = merged$I,
         R = merged$R,
         NI = merged$NI,
-        total = merged$S + merged$SDD + merged$I + merged$R + merged$NI,
-        total_rows = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$na,
+        WT = merged$WT,
+        NWT = merged$NWT,
+        NS = merged$NS,
+        total = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$WT + merged$NWT + merged$NS,
+        total_rows = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$WT + merged$NWT + merged$NS + merged$na,
         stringsAsFactors = FALSE
       )
       if (data_has_groups) {
@@ -229,12 +237,17 @@ format.bug_drug_combinations <- function(x,
       I = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$I[i], na.rm = TRUE)),
       R = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)),
       NI = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NI[i], na.rm = TRUE)),
+      WT = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$WT[i], na.rm = TRUE)),
+      NWT = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NWT[i], na.rm = TRUE)),
+      NS = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NS[i], na.rm = TRUE)),
       total = vapply(FUN.VALUE = double(1), idx, function(i) {
         sum(x$S[i], na.rm = TRUE) +
           sum(x$SDD[i], na.rm = TRUE) +
           sum(x$I[i], na.rm = TRUE) +
           sum(x$R[i], na.rm = TRUE) +
-          sum(x$NI[i], na.rm = TRUE)
+          sum(x$WT[i], na.rm = TRUE) +
+          sum(x$NWT[i], na.rm = TRUE) +
+          sum(x$NS[i], na.rm = TRUE)
       }),
       stringsAsFactors = FALSE
     )
@@ -246,10 +259,10 @@ format.bug_drug_combinations <- function(x,
   if (remove_intrinsic_resistant == TRUE) {
     x <- subset(x, R != total)
   }
+
+  x$isolates <- x$R + x$NWT
   if (combine_SI == TRUE) {
-    x$isolates <- x$R
-  } else {
-    x$isolates <- x$R + x$I + x$SDD
+    x$isolates <- x$isolates + x$I + x$SDD
   }
 
   give_ab_name <- function(ab, format, language) {

R/count.R

@@ -33,13 +33,16 @@
 #'
 #' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
 #' @param ... One or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.sir()] if needed.
+#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
+#'   * EUCAST: [count_susceptible()] \eqn{= N_{S} + N_{I}}, [count_resistant()] \eqn{= N_{R}}
+#'   * CLSI: [count_susceptible()] \eqn{= N_{S} + N_{SDD}}, [count_resistant()] \eqn{= N_{I} + N_{R}}
+#'
+#' You can also use e.g. [count_R()] or [count_S()] instead, to be explicit.
 #' @inheritParams proportion
 #' @inheritSection as.sir Interpretation of SIR
 #' @details These functions are meant to count isolates. Use the [resistance()]/[susceptibility()] functions to calculate microbial resistance/susceptibility.
 #'
-#' The function [count_resistant()] is equal to the function [count_R()]. The function [count_susceptible()] is equal to the function [count_SI()].
-#'
-#' The function [n_sir()] is an alias of [count_all()]. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to `n_distinct()`. Their function is equal to `count_susceptible(...) + count_resistant(...)`.
+#' The function [n_sir()] is an alias of [count_all()]. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to `dplyr`'s `n_distinct()`. Their function is equal to `count_susceptible(...) + count_resistant(...)`.
 #'
 #' The function [count_df()] takes any variable from `data` that has an [`sir`] class (created with [as.sir()]) and counts the number of S's, I's and R's. It also supports grouped variables. The function [sir_df()] works exactly like [count_df()], but adds the percentage of S, I and R.
 #' @inheritSection proportion Combination Therapy
@@ -119,10 +122,21 @@
 #'     count_df(translate = FALSE)
 #' }
 #' }
-count_resistant <- function(..., only_all_tested = FALSE) {
+count_resistant <- function(...,
+                            only_all_tested = FALSE,
+                            guideline = getOption("AMR_guideline", "EUCAST")) {
+  # other arguments for meet_criteria are handled by sir_calc()
+  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
+    message_("`count_resistant()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("This message will be shown once per session.")
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = "R",
+      ab_result = c(
+        "R", "NWT", "NS",
+        if (identical(guideline, "CLSI")) "I"
+      ),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -132,10 +146,21 @@ count_resistant <- function(..., only_all_tested = FALSE) {
 
 #' @rdname count
 #' @export
-count_susceptible <- function(..., only_all_tested = FALSE) {
+count_susceptible <- function(...,
+                              only_all_tested = FALSE,
+                              guideline = getOption("AMR_guideline", "EUCAST")) {
+  # other arguments for meet_criteria are handled by sir_calc()
+  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
+    message_("`count_susceptible()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("This message will be shown once per session.")
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "SDD", "I"),
+      ab_result = c(
+        "S", "SDD", "WT",
+        if (identical(guideline, "EUCAST")) "I"
+      ),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -161,7 +186,7 @@ count_S <- function(..., only_all_tested = FALSE) {
 count_SI <- function(..., only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "SDD", "I"),
+      ab_result = c("S", "SDD", "I", "WT"),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -187,7 +212,7 @@ count_I <- function(..., only_all_tested = FALSE) {
 count_IR <- function(..., only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = c("I", "SDD", "R"),
+      ab_result = c("I", "SDD", "R", "NWT"),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -200,7 +225,7 @@ count_IR <- function(..., only_all_tested = FALSE) {
 count_R <- function(..., only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = "R",
+      ab_result = c("R", "NWT", "NS"),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -213,7 +238,7 @@ count_R <- function(..., only_all_tested = FALSE) {
 count_all <- function(..., only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "SDD", "I", "R", "NI"),
+      ab_result = VALID_SIR_LEVELS,
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),

R/custom_eucast_rules.R

@@ -220,8 +220,8 @@ custom_eucast_rules <- function(...) {
     result_value <- as.character(result)[[3]]
     result_value[result_value == "NA"] <- NA
     stop_ifnot(
-      result_value %in% c("S", "SDD", "I", "R", "NI", NA),
-      "the resulting value of rule ", i, " must be either \"S\", \"SDD\", \"I\", \"R\", \"NI\" or NA"
+      result_value %in% c(VALID_SIR_LEVELS, NA),
+      paste0("the resulting value of rule ", i, " must be either ", vector_or(c(VALID_SIR_LEVELS, NA), sort = FALSE))
     )
     result_value <- as.sir(result_value)
 

R/data.R

@@ -38,7 +38,7 @@
 #' - `ab`\cr antimicrobial ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. ***This is a unique identifier.***
 #' - `cid`\cr Compound ID as found in PubChem. ***This is a unique identifier.***
 #' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO. ***This is a unique identifier.***
-#' - `group`\cr A short and concise group name, based on WHONET and WHOCC definitions
+#' - `group`\cr One or more short and concise group names, based on WHONET and WHOCC definitions
 #' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02` (last updated `r documentation_date(TAXONOMY_VERSION$ATC_DDD$accessed_date)`):
 #' - `atc_group1`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like `"Macrolides, lincosamides and streptogramins"`
 #' - `atc_group2`\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like `"Macrolides"`
@@ -282,7 +282,7 @@
 
 #' Data Set with Clinical Breakpoints for SIR Interpretation
 #'
-#' @description Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, `r length(unique(clinical_breakpoints$host[!clinical_breakpoints$host %in% clinical_breakpoints$type]))` different animal groups, and ECOFFs.
+#' @description Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This data set contains breakpoints for humans, `r length(unique(clinical_breakpoints$host[!clinical_breakpoints$host %in% clinical_breakpoints$type]))` different animal groups, and ECOFFs.
 #'
 #' These breakpoints are currently implemented:
 #' - For **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
@@ -368,7 +368,7 @@
 #' @format A [tibble][tibble::tibble] with `r format(nrow(esbl_isolates), big.mark = " ")` observations and `r ncol(esbl_isolates)` variables:
 #' - `esbl`\cr Logical indicator if the isolate is ESBL-producing
 #' - `genus`\cr Genus of the microorganism
-#' - `AMC:COL`\cr MIC values for 17 antimicrobial agents, transformed to class [`mic`] (see [as.mic()])
+#' - `AMC:COL`\cr MIC values for 17 antimicrobial drugs, transformed to class [`mic`] (see [as.mic()])
 #' @details See our [tidymodels integration][amr-tidymodels] for an example using this data set.
 #' @examples
 #' esbl_isolates

R/disk.R

@@ -121,7 +121,7 @@ as.disk <- function(x, na.rm = FALSE) {
       cur_col <- get_current_column()
       warning_("in `as.disk()`: ", na_after - na_before, " result",
         ifelse(na_after - na_before > 1, "s", ""),
-        ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
+        ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
         " truncated (",
         round(((na_after - na_before) / length(x)) * 100),
         "%) that were invalid disk zones: ",
@@ -236,12 +236,14 @@ rep.disk <- function(x, ...) {
 # this prevents the requirement for putting the dependency in Imports:
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
 get_skimmers.disk <- function(column) {
+  column <- as.integer(column)
   skimr::sfl(
     skim_type = "disk",
-    min = ~ min(as.double(.), na.rm = TRUE),
-    max = ~ max(as.double(.), na.rm = TRUE),
-    median = ~ stats::median(as.double(.), na.rm = TRUE),
-    n_unique = ~ length(unique(stats::na.omit(.))),
-    hist = ~ skimr::inline_hist(stats::na.omit(as.double(.)))
+    p0 = ~ stats::quantile(column, probs = 0, na.rm = TRUE, names = FALSE),
+    p25 = ~ stats::quantile(column, probs = 0.25, na.rm = TRUE, names = FALSE),
+    p50 = ~ stats::quantile(column, probs = 0.5, na.rm = TRUE, names = FALSE),
+    p75 = ~ stats::quantile(column, probs = 0.75, na.rm = TRUE, names = FALSE),
+    p100 = ~ stats::quantile(column, probs = 1, na.rm = TRUE, names = FALSE),
+    hist = ~ skimr::inline_hist(stats::na.omit(column), 10)
   )
 }

R/first_isolate.R

@@ -61,7 +61,7 @@
 #'
 #' All isolates with a microbial ID of `NA` will be excluded as first isolate.
 #'
-#' ### Different methods
+#' ## Different methods
 #'
 #' According to previously-mentioned sources, there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies).
 #'
@@ -89,21 +89,29 @@
 #' | - Major difference in any antimicrobial result   | - `first_isolate(x, type = "points")`                 |
 #' | - Any difference in key antimicrobial results    | - `first_isolate(x, type = "keyantimicrobials")`      |
 #'
-#' ### Isolate-based
+#' **Isolate-based**
+#'
+#' _Minimum variables required: Microorganism identifier_
 #'
 #' This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the [first_isolate()] function. For example, the default setting for `include_unknown` (`FALSE`) will omit selection of rows without a microbial ID.
 #'
-#' ### Patient-based
+#' **Patient-based**
 #'
-#' To include every genus-species combination per patient once, set the `episode_days` to `Inf`. This method makes sure that no duplicate isolates are selected from the same patient. This method is preferred to e.g. identify the first MRSA finding of each patient to determine the incidence. Conversely, in a large longitudinal data set, this could mean that isolates are *excluded* that were found years after the initial isolate.
+#' _Minimum variables required: Microorganism identifier, Patient identifier_
 #'
-#' ### Episode-based
+#' This method includes every genus-species combination per patient once. This method makes sure that no duplicate isolates are selected from the same patient. This method is preferred to e.g. identify the first MRSA finding of each patient to determine the incidence. Conversely, in a large longitudinal data set, this could mean that isolates are *excluded* that were found years after the initial isolate.
 #'
-#' To include every genus-species combination per patient episode once, set the `episode_days` to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data or ICU cases, long episodes are common for analysing regional and national data.
+#' **Episode-based**
+#'
+#' _Minimum variables required: Microorganism identifier, Patient identifier, Date_
+#'
+#' To include every genus-species combination per patient episode once, set the `episode_days` to a sensible number of days. Depending on the type of analysis, this could be e.g., 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data or ICU cases, long episodes are common for analysing regional and national data.
 #'
 #' This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant *Staphylococcus aureus* (MRSA) isolate cannot be differentiated from a wildtype *Staphylococcus aureus* isolate.
 #'
-#' ### Phenotype-based
+#' **Phenotype-based**
+#'
+#' _Minimum variables required: Microorganism identifier, Patient identifier, Date, Antimicrobial test results_
 #'
 #' This is a more reliable method, since it also *weighs* the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
 #'
@@ -238,7 +246,7 @@ first_isolate <- function(x = NULL,
     FUN.VALUE = logical(1),
     X = x,
     # check only first 10,000 rows
-    FUN = function(x) any(as.character(x[1:10000]) %in% c("S", "SDD", "I", "R", "NI"), na.rm = TRUE),
+    FUN = function(x) any(as.character(x[1:10000]) %in% VALID_SIR_LEVELS, na.rm = TRUE),
     USE.NAMES = FALSE
   ))
   if (method == "phenotype-based" && !any_col_contains_sir) {

R/interpretive_rules.R

@@ -53,15 +53,21 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
   vector_and(txt, quotes = FALSE)
 }
 
-#' Apply EUCAST Rules
+#' Apply Interpretive Rules
 #'
 #' @description
-#' Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
+#' **WORK IN PROGRESS**
 #'
-#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
+# TODO Remove this remark before next release
+#' **The `interpretive_rules()` function is new, to allow CLSI 'rules' too. The old `eucast_rules()` function will stay as a wrapper, but we need to generalise more parts of the underlying code to allow more than just EUCAST.**
+#'
+#' Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
+#'
+#' To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see *Details*.
 #' @param x A data set with antimicrobials columns, such as `amox`, `AMX` and `AMC`.
 #' @param info A [logical] to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.
-#' @param rules A [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expected_phenotypes"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option [`AMR_eucastrules`][AMR-options]: `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
+#' @param guideline A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option [`AMR_guideline`][AMR-options].
+#' @param rules A [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expected_phenotypes"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option [`AMR_interpretive_rules`][AMR-options]: `options(AMR_interpretive_rules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
 #' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
 #' @param version_breakpoints The version number to use for the EUCAST Clinical Breakpoints guideline. Can be `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
 #' @param version_expected_phenotypes The version number to use for the EUCAST Expected Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_EXPECTED_PHENOTYPES), reverse = TRUE)`.
@@ -100,9 +106,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #'
 #' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
 #'
-#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option [`AMR_eucastrules`][AMR-options], i.e. run `options(AMR_eucastrules = "all")`.
+#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option [`AMR_interpretive_rules`][AMR-options], i.e. run `options(AMR_interpretive_rules = "all")`.
 #' @aliases EUCAST
-#' @rdname eucast_rules
+#' @rdname interpretive_rules
 #' @export
 #' @return The input of `x`, possibly with edited values of antimicrobials. Or, if `verbose = TRUE`, a [data.frame] with all original and new values of the affected bug-drug combinations.
 #' @source
@@ -156,10 +162,11 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' eucast_dosage(c("tobra", "genta", "cipro"), "iv")
 #'
 #' eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
-eucast_rules <- function(x,
+interpretive_rules <- function(x,
                                col_mo = NULL,
                                info = interactive(),
-                         rules = getOption("AMR_eucastrules", default = c("breakpoints", "expected_phenotypes")),
+                               rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
+                               guideline = getOption("AMR_guideline", "EUCAST"),
                                verbose = FALSE,
                                version_breakpoints = 15.0,
                                version_expected_phenotypes = 1.2,
@@ -171,6 +178,7 @@ eucast_rules <- function(x,
                                ...) {
   meet_criteria(x, allow_class = "data.frame")
   meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
+  meet_criteria(guideline, allow_class = "character", has_length = 1, is_in = c("EUCAST", "CLSI"))
   meet_criteria(info, allow_class = "logical", has_length = 1)
   meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5, 6), is_in = c("breakpoints", "expected_phenotypes", "expert", "other", "all", "custom"))
   meet_criteria(verbose, allow_class = "logical", has_length = 1)
@@ -182,6 +190,11 @@ eucast_rules <- function(x,
   meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
   meet_criteria(overwrite, allow_class = "logical", has_length = 1)
 
+  stop_if(
+    guideline == "CLSI",
+    "CLSI guideline is not yet supported."
+  )
+
   stop_if(
     !is.na(ampc_cephalosporin_resistance) && !any(c("expert", "all") %in% rules),
     "For the `ampc_cephalosporin_resistance` argument to work, the `rules` argument must contain `\"expert\"` or `\"all\"`."
@@ -1092,6 +1105,29 @@ eucast_rules <- function(x,
   }
 }
 
+#' @rdname interpretive_rules
+#' @export
+eucast_rules <- function(x,
+                         col_mo = NULL,
+                         info = interactive(),
+                         rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
+                         ...) {
+  if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
+    warning_("The global option `AMR_eucastrules` that you have set is now invalid was ignored - set `AMR_interpretive_rules` instead. See `?AMR-options`.")
+  }
+  interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
+}
+
+#' @rdname interpretive_rules
+#' @export
+clsi_rules <- function(x,
+                       col_mo = NULL,
+                       info = interactive(),
+                       rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
+                       ...) {
+  interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "CLSI", ...)
+}
+
 # helper function for editing the table ----
 edit_sir <- function(x,
                      to,
@@ -1131,7 +1167,7 @@ edit_sir <- function(x,
       track_changes$sir_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir)]
     }
     isNA <- is.na(new_edits[rows, cols])
-    isSIR <- !isNA & (new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
+    isSIR <- !isNA & (new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI" | new_edits[rows, cols] == "WT" | new_edits[rows, cols] == "NWT" | new_edits[rows, cols] == "NS")
     non_SIR <- !isSIR
     if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) {
       warning_("Some values had SIR values and were not overwritten, since `overwrite = FALSE`.")
@@ -1230,7 +1266,7 @@ edit_sir <- function(x,
   return(track_changes)
 }
 
-#' @rdname eucast_rules
+#' @rdname interpretive_rules
 #' @export
 eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 15) {
   meet_criteria(ab, allow_class = c("character", "numeric", "integer", "factor"))

R/key_antimicrobials.R

@@ -282,6 +282,9 @@ generate_antimicrobials_string <- function(df) {
           function(x) {
             x <- toupper(as.character(x))
             x[x == "SDD"] <- "I"
+            x[x == "WT"] <- "S"
+            x[x == "NWT"] <- "R"
+            x[x == "NS"] <- "R"
             # ignore "NI" here, no use for determining first isolates
             x[!x %in% c("S", "I", "R")] <- "."
             paste(x)
@@ -312,9 +315,7 @@ antimicrobials_equal <- function(y,
   key2sir <- function(val) {
     val <- strsplit(val, "", fixed = TRUE)[[1L]]
     val.int <- rep(NA_real_, length(val))
-    val.int[val == "S"] <- 1
-    val.int[val %in% c("I", "SDD")] <- 2
-    val.int[val == "R"] <- 3
+    val.int[val %in% VALID_SIR_LEVELS] <- as.double(as.sir(val[val %in% VALID_SIR_LEVELS]))
     val.int
   }
   # only run on uniques

R/mdro.R

@@ -41,7 +41,7 @@
 #' @inheritParams eucast_rules
 #' @param pct_required_classes Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
 #' @param combine_SI A [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
-#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
+#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
 #' @details
 #' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
 #'
@@ -174,48 +174,23 @@ mdro <- function(x = NULL,
   }
 
   # get gene values as TRUE/FALSE
-  if (is.character(esbl)) {
-    meet_criteria(esbl, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    esbl <- x[[esbl]]
-    meet_criteria(esbl, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(esbl) == 1) {
-    esbl <- rep(esbl, NROW(x))
+  resolve_gene_var <- function(x, gene, varname) {
+    if (is.character(gene)) {
+      meet_criteria(gene, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
+      gene <- x[[gene]]
+      meet_criteria(gene, allow_class = "logical", allow_NA = TRUE)
+    } else if (length(gene) == 1) {
+      gene <- rep(gene, NROW(x))
     }
-  if (is.character(carbapenemase)) {
-    meet_criteria(carbapenemase, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    carbapenemase <- x[[carbapenemase]]
-    meet_criteria(carbapenemase, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(carbapenemase) == 1) {
-    carbapenemase <- rep(carbapenemase, NROW(x))
-  }
-  if (is.character(mecA)) {
-    meet_criteria(mecA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    mecA <- x[[mecA]]
-    meet_criteria(mecA, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(mecA) == 1) {
-    mecA <- rep(mecA, NROW(x))
-  }
-  if (is.character(mecC)) {
-    meet_criteria(mecC, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    mecC <- x[[mecC]]
-    meet_criteria(mecC, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(mecC) == 1) {
-    mecC <- rep(mecC, NROW(x))
-  }
-  if (is.character(vanA)) {
-    meet_criteria(vanA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    vanA <- x[[vanA]]
-    meet_criteria(vanA, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(vanA) == 1) {
-    vanA <- rep(vanA, NROW(x))
-  }
-  if (is.character(vanB)) {
-    meet_criteria(vanB, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    vanB <- x[[vanB]]
-    meet_criteria(vanB, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(vanB) == 1) {
-    vanB <- rep(vanB, NROW(x))
+    x[[varname]] <- gene
+    x
   }
+  x <- resolve_gene_var(x, esbl, "esbl")
+  x <- resolve_gene_var(x, carbapenemase, "carbapenemase")
+  x <- resolve_gene_var(x, mecA, "mecA")
+  x <- resolve_gene_var(x, mecC, "mecC")
+  x <- resolve_gene_var(x, vanA, "vanA")
+  x <- resolve_gene_var(x, vanB, "vanB")
 
   info.bak <- info
   # don't throw info's more than once per call
@@ -772,7 +747,7 @@ mdro <- function(x = NULL,
         )
       }
       x[rows_to_change, "MDRO"] <<- to
-      x[rows_to_change, "reason"] <<- reason
+      x[rows_to_change, "reason"] <<- paste0(x[rows_to_change, "reason", drop = TRUE], "; ", reason)
       x[rows_not_to_change, "reason"] <<- "guideline criteria not met"
     }
   }
@@ -802,7 +777,7 @@ mdro <- function(x = NULL,
           sum(vapply(
             FUN.VALUE = logical(1),
             group_tbl,
-            function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "SDD", "I", "R"))
+            function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% VALID_SIR_LEVELS[VALID_SIR_LEVELS != "NI"])
           ))
         }
       )
@@ -854,7 +829,7 @@ mdro <- function(x = NULL,
   x <- left_join_microorganisms(x, by = col_mo)
   x$MDRO <- ifelse(!is.na(x$genus), 1, NA_integer_)
   x$row_number <- seq_len(nrow(x))
-  x$reason <- NA_character_
+  x$reason <- ""
   x$all_nonsusceptible_columns <- ""
 
   if (guideline$code == "cmi2012") {
@@ -1498,7 +1473,7 @@ mdro <- function(x = NULL,
     }
     trans_tbl(
       3, # positive
-      rows = which(x$order == "Enterobacterales" & esbl == TRUE),
+      rows = which(x$order == "Enterobacterales" & x$esbl == TRUE),
       cols = "any",
       any_all = "any",
       reason = "Enterobacterales: ESBL"
@@ -1519,17 +1494,18 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      rows = which(x$order == "Enterobacterales" & carbapenemase == TRUE),
+      rows = which(x$order == "Enterobacterales" & x$carbapenemase == TRUE),
       cols = "any",
       any_all = "any",
       reason = "Enterobacterales: carbapenemase"
     )
+    c.freundii_complex <- AMR::microorganisms.groups$mo_name[AMR::microorganisms.groups$mo_group_name == "Citrobacter freundii complex"]
     trans_tbl(
       3,
       rows = which(col_values(x, SXT) == "R" &
         (col_values(x, GEN) == "R" | col_values(x, TOB) == "R" | col_values(x, AMK) == "R") &
         (col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R") &
-        (x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c("Citrobacter freundii", "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
+        (x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c(c.freundii_complex, "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
       cols = c(SXT, aminoglycosides, fluoroquinolones),
       any_all = "any",
       reason = "Enterobacterales group II: aminoglycoside + fluoroquinolone + cotrimoxazol"
@@ -1557,14 +1533,14 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       2, # unconfirmed
-      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(carbapenemase)),
+      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(x$carbapenemase)),
       cols = carbapenems,
       any_all = "any",
       reason = "A. baumannii-calcoaceticus complex: potential carbapenemase"
     )
     trans_tbl(
       3,
-      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & carbapenemase == TRUE),
+      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & x$carbapenemase == TRUE),
       cols = carbapenems,
       any_all = "any",
       reason = "A. baumannii-calcoaceticus complex: carbapenemase"
@@ -1574,6 +1550,7 @@ mdro <- function(x = NULL,
     x$psae <- 0
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, TOB) == "R") | NA_as_FALSE(col_values(x, AMK) == "R"), 1, 0)
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, IPM) == "R") | NA_as_FALSE(col_values(x, MEM) == "R"), 1, 0)
+    x$psae <- x$psae + ifelse(NA_as_FALSE(x$carbapenemase), 1, 0)
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R") | NA_as_FALSE(col_values(x, TZP) == "R"), 1, 0)
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CAZ) == "R") | NA_as_FALSE(col_values(x, CZA) == "R"), 1, 0)
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R") | NA_as_FALSE(col_values(x, NOR) == "R") | NA_as_FALSE(col_values(x, LVX) == "R"), 1, 0)
@@ -1602,7 +1579,7 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (vanA == TRUE | vanB == TRUE)),
+      rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (x$vanA == TRUE | x$vanB == TRUE)),
       cols = c(PEN, AMX, AMP, VAN),
       any_all = "any",
       reason = "E. faecium: vanA/vanB gene + penicillin group"
@@ -1611,14 +1588,14 @@ mdro <- function(x = NULL,
     # Staphylococcus aureus complex (= aureus, argenteus or schweitzeri)
     trans_tbl(
       2,
-      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(mecA) | is.na(mecC))),
+      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(x$mecA) | is.na(x$mecC))),
       cols = c(AMC, TZP, FLC, OXA, FOX, FOX1),
       any_all = "any",
       reason = "S. aureus complex: potential MRSA"
     )
     trans_tbl(
       3,
-      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (mecA == TRUE | mecC == TRUE)),
+      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (x$mecA == TRUE | x$mecC == TRUE)),
       cols = "any",
       any_all = "any",
       reason = "S. aureus complex: mecA/mecC gene"
@@ -1899,6 +1876,10 @@ mdro <- function(x = NULL,
     # fill in empty reasons
     x$reason[is.na(x$reason)] <- "not covered by guideline"
     x[rows_empty, "reason"] <- paste(x[rows_empty, "reason"], "(note: no available test results)")
+    # starting semicolons must be removed
+    x$reason <- trimws(gsub("^;", "", x$reason))
+    # if criteria were not met initially, but later they were, then they have a following semicolon; remove the initial lack of meeting criteria
+    x$reason <- trimws(gsub("guideline criteria not met;", "", x$reason, fixed = TRUE))
     # format data set
     colnames(x)[colnames(x) == col_mo] <- "microorganism"
     x$microorganism <- mo_name(x$microorganism, language = NULL)

R/mean_amr_distance.R

@@ -118,7 +118,7 @@ mean_amr_distance.disk <- function(x, ...) {
 mean_amr_distance.sir <- function(x, ..., combine_SI = TRUE) {
   meet_criteria(combine_SI, allow_class = "logical", has_length = 1, .call_depth = -1)
   if (isTRUE(combine_SI)) {
-    x[x %in% c("I", "SDD")] <- "S"
+    x[x %in% c("I", "SDD")] <- "S" # do not acknowledge CLSI/EUCAST guideline here to keep the numeric mean_amr_distance consistent between systems
   }
   mean_amr_distance(as.double(x))
 }

R/mic.R

@@ -63,6 +63,7 @@ COMMON_MIC_VALUES <- c(
 #' @param x A [character] or [numeric] vector.
 #' @param na.rm A [logical] indicating whether missing values should be removed.
 #' @param keep_operators A [character] specifying how to handle operators (such as `>` and `<=`) in the input. Accepts one of three values: `"all"` (or `TRUE`) to keep all operators, `"none"` (or `FALSE`) to remove all operators, or `"edges"` to keep operators only at both ends of the range.
+#' @param round_to_next_log2 A [logical] to round up all values to the next log2 level, that are not either `r vector_or(COMMON_MIC_VALUES, quotes = F)`. Values that are already in this list (with or without operators), are left unchanged (including any operators).
 #' @param ... Arguments passed on to methods.
 #' @details To interpret MIC values as SIR values, use [as.sir()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
 #'
@@ -157,10 +158,12 @@ COMMON_MIC_VALUES <- c(
 #' if (require("ggplot2")) {
 #'   autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
 #' }
-as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
+as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2 = FALSE) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
   meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)
+  meet_criteria(round_to_next_log2, allow_class = "logical", has_length = 1)
+
   if (isTRUE(keep_operators)) {
     keep_operators <- "all"
   } else if (isFALSE(keep_operators)) {
@@ -168,6 +171,9 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
   }
 
   if (is.mic(x) && (keep_operators == "all" || !any(x %like% "[>=<]", na.rm = TRUE))) {
+    if (isTRUE(round_to_next_log2)) {
+      x <- roundup_to_nearest_log2(x)
+    }
     if (!identical(levels(x), VALID_MIC_LEVELS)) {
       # might be from an older AMR version - just update MIC factor levels
       x <- set_clean_class(factor(as.character(x), levels = VALID_MIC_LEVELS, ordered = TRUE),
@@ -260,7 +266,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
     cur_col <- get_current_column()
     warning_("in `as.mic()`: ", na_after - na_before, " result",
       ifelse(na_after - na_before > 1, "s", ""),
-      ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
+      ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
       " truncated (",
       round(((na_after - na_before) / length(x)) * 100),
       "%) that were invalid MICs: ",
@@ -279,6 +285,10 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
     x[!x %in% keep] <- gsub("[>=<]", "", x[!x %in% keep])
   }
 
+  if (isTRUE(round_to_next_log2)) {
+    x <- roundup_to_nearest_log2(x)
+  }
+
   set_clean_class(factor(x, levels = VALID_MIC_LEVELS, ordered = TRUE),
     new_class = c("mic", "ordered", "factor")
   )
@@ -305,7 +315,7 @@ NA_mic_ <- set_clean_class(factor(NA, levels = VALID_MIC_LEVELS, ordered = TRUE)
 #' @rdname as.mic
 #' @param mic_range A manual range to rescale the MIC values, e.g., `mic_range = c(0.001, 32)`. Use `NA` to prevent rescaling on one side, e.g., `mic_range = c(NA, 32)`.
 #' @export
-rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
+rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE, round_to_next_log2 = FALSE) {
   meet_criteria(mic_range, allow_class = c("numeric", "integer", "logical", "mic"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)
   if (is.numeric(mic_range)) {
     mic_range <- trimws(format(mic_range, scientific = FALSE))
@@ -336,7 +346,7 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
     x[x > max_mic] <- max_mic
   }
 
-  x <- as.mic(x, keep_operators = ifelse(keep_operators == "edges", "none", keep_operators))
+  x <- as.mic(x, keep_operators = ifelse(keep_operators == "edges", "none", keep_operators), round_to_next_log2 = round_to_next_log2)
 
   if (isTRUE(as.mic)) {
     if (keep_operators == "edges" && length(unique(x)) > 1) {
@@ -596,15 +606,33 @@ get_skimmers.mic <- function(column) {
   column <- as.mic(column) # make sure that currently implemented MIC levels are used
   skimr::sfl(
     skim_type = "mic",
-    p0 = ~ stats::quantile(., probs = 0, na.rm = TRUE, names = FALSE),
-    p25 = ~ stats::quantile(., probs = 0.25, na.rm = TRUE, names = FALSE),
-    p50 = ~ stats::quantile(., probs = 0.5, na.rm = TRUE, names = FALSE),
-    p75 = ~ stats::quantile(., probs = 0.75, na.rm = TRUE, names = FALSE),
-    p100 = ~ stats::quantile(., probs = 1, na.rm = TRUE, names = FALSE),
-    hist = ~ skimr::inline_hist(log2(stats::na.omit(.)), 5)
+    p0 = ~ stats::quantile(column, probs = 0, na.rm = TRUE, names = FALSE),
+    p25 = ~ stats::quantile(column, probs = 0.25, na.rm = TRUE, names = FALSE),
+    p50 = ~ stats::quantile(column, probs = 0.5, na.rm = TRUE, names = FALSE),
+    p75 = ~ stats::quantile(column, probs = 0.75, na.rm = TRUE, names = FALSE),
+    p100 = ~ stats::quantile(column, probs = 1, na.rm = TRUE, names = FALSE),
+    hist = ~ skimr::inline_hist(log2(stats::na.omit(column)), 10)
   )
 }
 
+
+roundup_to_nearest_log2 <- function(x) {
+  x_dbl <- suppressWarnings(as.double(gsub("[>=<]", "", x)))
+  x_new <- vapply(
+    FUN.VALUE = double(1),
+    x_dbl,
+    function(val) {
+      if (is.na(val)) {
+        NA_real_
+      } else {
+        COMMON_MIC_VALUES[which(COMMON_MIC_VALUES >= val)][1]
+      }
+    }
+  )
+  x[!x_dbl %in% COMMON_MIC_VALUES] <- x_new[!x_dbl %in% COMMON_MIC_VALUES]
+  x
+}
+
 # Miscellaneous mathematical functions ------------------------------------
 
 #' @method mean mic

R/mo.R

@@ -675,7 +675,7 @@ pillar_shaft.mo <- function(x, ...) {
   }
 
   # add the names to the bugs as mouse-over!
-  if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
+  if (in_rstudio()) {
     out[!x %in% c("UNKNOWN", NA)] <- font_url(
       url = paste0(
         x[!x %in% c("UNKNOWN", NA)], ": ",
@@ -747,13 +747,17 @@ freq.mo <- function(x, ...) {
 # this prevents the requirement for putting the dependency in Imports:
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)
 get_skimmers.mo <- function(column) {
+  mo <- as.mo(column, keep_synonyms = TRUE, language = NULL, info = FALSE)
+  mo <- mo[!is.na(mo)]
+  spp <- mo[mo_species(mo, keep_synonyms = TRUE, language = NULL, info = FALSE) != ""]
   skimr::sfl(
     skim_type = "mo",
-    unique_total = ~ length(unique(stats::na.omit(.))),
-    gram_negative = ~ sum(mo_is_gram_negative(.), na.rm = TRUE),
-    gram_positive = ~ sum(mo_is_gram_positive(.), na.rm = TRUE),
-    top_genus = ~ names(sort(-table(mo_genus(stats::na.omit(.), language = NULL))))[1L],
-    top_species = ~ names(sort(-table(mo_name(stats::na.omit(.), language = NULL))))[1L]
+    n_unique = ~ length(unique(mo)),
+    gram_negative = ~ sum(mo_is_gram_negative(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
+    gram_positive = ~ sum(mo_is_gram_positive(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
+    yeast = ~ sum(mo_is_yeast(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
+    top_genus = ~ names(sort(-table(mo_genus(mo, keep_synonyms = TRUE, language = NULL, info = FALSE))))[1L],
+    top_species = ~ names(sort(-table(mo_name(spp, keep_synonyms = TRUE, language = NULL, info = FALSE))))[1L],
   )
 }
 

R/plotting.R

@@ -52,11 +52,19 @@
 #' @details
 #' ### The `scale_*_mic()` Functions
 #'
-#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the operators in MIC values (such as `>=`) if desired. Missing intermediate log2 levels will be plotted too.
+#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale.
+#'
+#' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [mic][as.mic()].
+#'
+#' When manually added though, they allow to rescale the MIC range with an 'inside' or 'outside' range if required, and provide the option to retain the operators in MIC values (such as `>=`). Missing intermediate log2 levels will always be plotted too.
 #'
 #' ### The `scale_*_sir()` Functions
 #'
-#' The functions [scale_x_sir()], [scale_colour_sir()], and [scale_fill_sir()] functions allow to plot the [sir][as.sir()] class in the right order (`r paste(levels(NA_sir_), collapse = " < ")`). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the `r length(AMR:::LANGUAGES_SUPPORTED)` supported languages (use `language = NULL` to keep S/I/R). Also, except for [scale_x_sir()], they set colour-blind friendly colours to the `colour` and `fill` aesthetics.
+#' The functions [scale_x_sir()], [scale_colour_sir()], and [scale_fill_sir()] functions allow to plot the [sir][as.sir()] class in the right order (`r paste(levels(NA_sir_), collapse = " < ")`).
+#'
+#' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [sir][as.sir()].
+#'
+#' At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the `r length(AMR:::LANGUAGES_SUPPORTED)` supported languages (use `language = NULL` to keep S/I/R). Also, except for [scale_x_sir()], they set colour-blind friendly colours to the `colour` and `fill` aesthetics.
 #'
 #' ### Additional `ggplot2` Functions
 #'
@@ -114,17 +122,12 @@
 #'   ) +
 #'     geom_col()
 #'   mic_plot +
-#'     labs(title = "without scale_x_mic()")
+#'     labs(title = "scale_x_mic() automatically applied")
 #' }
 #' if (require("ggplot2")) {
 #'   mic_plot +
-#'     scale_x_mic() +
-#'     labs(title = "with scale_x_mic()")
-#' }
-#' if (require("ggplot2")) {
-#'   mic_plot +
-#'     scale_x_mic(keep_operators = "all") +
-#'     labs(title = "with scale_x_mic() keeping all operators")
+#'     scale_x_mic(keep_operators = "none") +
+#'     labs(title = "with scale_x_mic() keeping no operators")
 #' }
 #' if (require("ggplot2")) {
 #'   mic_plot +
@@ -151,7 +154,7 @@
 #'   ) +
 #'     geom_boxplot() +
 #'     geom_violin(linetype = 2, colour = "grey30", fill = NA) +
-#'     scale_y_mic()
+#'     labs(title = "scale_y_mic() automatically applied")
 #' }
 #' if (require("ggplot2")) {
 #'   ggplot(
@@ -183,7 +186,7 @@
 #'
 #' # Plotting using scale_y_mic() and scale_colour_sir() ------------------
 #' if (require("ggplot2")) {
-#'   plain <- ggplot(
+#'   mic_sir_plot <- ggplot(
 #'     data.frame(
 #'       mic = some_mic_values,
 #'       group = some_groups,
@@ -197,21 +200,16 @@
 #'     theme_minimal() +
 #'     geom_boxplot(fill = NA, colour = "grey30") +
 #'     geom_jitter(width = 0.25)
+#'     labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
 #'
-#'   plain
+#'   mic_sir_plot
 #' }
 #' if (require("ggplot2")) {
-#'   # and now with our MIC and SIR scale functions:
-#'   plain +
-#'     scale_y_mic() +
-#'     scale_colour_sir()
-#' }
-#' if (require("ggplot2")) {
-#'   plain +
+#'   mic_sir_plot +
 #'     scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
 #'     scale_colour_sir(
-#'       language = "pt",
-#'       name = "Support in 27 languages"
+#'       language = "pt", # Portuguese
+#'       name = "Support in 28 languages"
 #'     )
 #' }
 #' }
@@ -229,6 +227,9 @@
 #' plot(some_sir_values)
 NULL
 
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::scale_type, mic)
+scale_type.mic <- function(x) c("mic", "discrete")
+
 create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
   ggplot_fn <- getExportedValue(paste0("scale_", aest, "_continuous"),
     ns = asNamespace("ggplot2")
@@ -247,6 +248,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
     as.double(rescale_mic(x = as.double(as.mic(x)), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE))
   }
   scale$transform_df <- function(self, df) {
+    out <- list()
     if (!aest %in% colnames(df)) {
       # support for geom_hline(), geom_vline(), etc
       other_x <- c("xintercept", "xmin", "xmax", "xend", "width")
@@ -258,11 +260,11 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       } else {
         stop_("No support for plotting df with `scale_", aest, "_mic()` with columns ", vector_and(colnames(df), sort = FALSE))
       }
-      out <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
-      if (!is.null(self$mic_values_rescaled) && any(out < min(self$mic_values_rescaled, na.rm = TRUE) | out > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
+      mics <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
+      if (!is.null(self$mic_values_rescaled) && any(mics < min(self$mic_values_rescaled, na.rm = TRUE) | mics > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
         warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
       }
-      df[[aest_val]] <- log2(as.double(out))
+      out[[aest_val]] <- log2(as.double(mics))
     } else {
       self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
       # create new breaks and labels here
@@ -283,14 +285,18 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
         self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
         self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
       }
-
       self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
-      if (aest == "y" && "group" %in% colnames(df) && "x" %in% colnames(df)) {
-        df$group <- as.integer(factor(df$x))
+
+      if (aest == "y" && "group" %in% colnames(df)) {
+        if (!"x" %in% colnames(df) || all(is.na(df$x))) {
+          out$group <- 1
+        } else {
+          out$group <- as.integer(factor(df$x))
         }
-      df[[aest]] <- self$mic_values_log
       }
-    df
+      out[[aest]] <- self$mic_values_log
+    }
+    out
   }
 
   scale$breaks <- function(..., self) {
@@ -317,7 +323,6 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       }
     }
   }
-
   scale$limits <- function(x, ..., self) {
     if (!is.null(self$mic_limits_set)) {
       if (is.function(self$mic_limits_set)) {
@@ -329,7 +334,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       rng <- range(log2(as.mic(self$mic_values_levels)))
       # add 0.5 extra space
       rng <- c(rng[1] - 0.5, rng[2] + 0.5)
-      if (!is.na(x[1]) && x[1] == 0) {
+      if (!is.null(x) && !is.na(x[1]) && x[1] == 0) {
         # scale that start at 0 must remain so, e.g. in case of geom_col()
         rng[1] <- 0
       }
@@ -377,6 +382,9 @@ scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
   create_scale_mic("fill", keep_operators = keep_operators, mic_range = mic_range, ...)
 }
 
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::scale_type, sir)
+scale_type.sir <- function(x) c("sir", "discrete")
+
 create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
   args <- list(...)
   args[c("value", "labels", "limits")] <- NULL
@@ -391,7 +399,12 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
       args,
       list(
         aesthetics = aesthetics,
-        values = c(colours_SIR, NI = "grey30")
+        values = c(colours_SIR,
+          NI = "grey30",
+          WT = unname(colours_SIR[1]),
+          NWT = unname(colours_SIR[4]),
+          NS = unname(colours_SIR[4])
+        )
       )
     )
   }
@@ -416,6 +429,9 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
       x[x == "SI"] <- "(S/I) Susceptible"
       x[x == "IR"] <- "(I/R) Non-susceptible"
       x[x == "NI"] <- "(NI) Non-interpretable"
+      x[x == "WT"] <- "(WT) Wildtype"
+      x[x == "NWT"] <- "(NWT) Non-wildtype"
+      x[x == "NS"] <- "(NS) Non-susceptible"
       x <- translate_AMR(x, language = language)
     }
     x
@@ -529,11 +545,16 @@ plot.mic <- function(x,
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
+  meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
+  meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)
 
   x <- as.mic(x) # make sure that currently implemented MIC levels are used
   main <- gsub(" +", " ", paste0(main, collapse = " "))
   colours_SIR <- expand_SIR_colours(colours_SIR)
 
+  # wildtype/Non-wildtype
+  is_wt_nwt <- identical(breakpoint_type, "ECOFF")
+
   x <- plotrange_as_table(x, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
@@ -564,10 +585,14 @@ plot.mic <- function(x,
   if (any(colours_SIR %in% cols_sub$cols)) {
     legend_txt <- character(0)
     legend_col <- character(0)
-    if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
+    if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
       legend_txt <- c(legend_txt, "(S) Susceptible")
       legend_col <- colours_SIR[1]
     }
+    if (is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
+      legend_txt <- c(legend_txt, "(WT) Wildtype")
+      legend_col <- colours_SIR[1]
+    }
     if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
       legend_txt <- c(legend_txt, "(SDD) Susceptible dose-dependent")
       legend_col <- c(legend_col, colours_SIR[2])
@@ -576,10 +601,14 @@ plot.mic <- function(x,
       legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
       legend_col <- c(legend_col, colours_SIR[3])
     }
-    if (any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
+    if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
       legend_txt <- c(legend_txt, "(R) Resistant")
       legend_col <- c(legend_col, colours_SIR[4])
     }
+    if (is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
+      legend_txt <- c(legend_txt, "(NWT) Non-wildtype")
+      legend_col <- c(legend_col, colours_SIR[4])
+    }
 
     legend("top",
       x.intersp = 0.5,
@@ -672,6 +701,8 @@ autoplot.mic <- function(object,
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
+  meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
+  meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)
 
   if ("main" %in% names(list(...))) {
     title <- list(...)$main
@@ -682,6 +713,9 @@ autoplot.mic <- function(object,
 
   colours_SIR <- expand_SIR_colours(colours_SIR)
 
+  # wildtype/Non-wildtype
+  is_wt_nwt <- identical(breakpoint_type, "ECOFF")
+
   object <- as.mic(object) # make sure that currently implemented MIC levels are used
   x <- plotrange_as_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
@@ -700,17 +734,21 @@ autoplot.mic <- function(object,
   df <- as.data.frame(x, stringsAsFactors = TRUE)
   colnames(df) <- c("mic", "count")
   df$cols <- cols_sub$cols
-  df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
+  df$cols[df$cols == colours_SIR[1] & !is_wt_nwt] <- "(S) Susceptible"
+  df$cols[df$cols == colours_SIR[1] & is_wt_nwt] <- "(WT) Wildtype"
   df$cols[df$cols == colours_SIR[2]] <- "(SDD) Susceptible dose-dependent"
   df$cols[df$cols == colours_SIR[3]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
-  df$cols[df$cols == colours_SIR[4]] <- "(R) Resistant"
+  df$cols[df$cols == colours_SIR[4] & !is_wt_nwt] <- "(R) Resistant"
+  df$cols[df$cols == colours_SIR[4] & is_wt_nwt] <- "(NWT) Non-wildtype"
   df$cols <- factor(translate_into_language(df$cols, language = language),
     levels = translate_into_language(
       c(
         "(S) Susceptible",
         "(SDD) Susceptible dose-dependent",
         paste("(I)", plot_name_of_I(cols_sub$guideline)),
-        "(R) Resistant"
+        "(R) Resistant",
+        "(WT) Wildtype",
+        "(NWT) Non-wildtype"
       ),
       language = language
     ),
@@ -725,7 +763,9 @@ autoplot.mic <- function(object,
       "(I) Susceptible, incr. exp." = colours_SIR[3],
       "(I) Intermediate" = colours_SIR[3],
       "(R) Resistant" = colours_SIR[4],
-      "(NI) Non-interpretable" = "grey30"
+      "(NI) Non-interpretable" = "grey30",
+      "(WT) Wildtype" = colours_SIR[1],
+      "(NWT) Non-wildtype" = colours_SIR[4]
     )
     names(vals) <- translate_into_language(names(vals), language = language)
     p <- p +
@@ -789,10 +829,15 @@ plot.disk <- function(x,
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
+  meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
+  meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)
 
   main <- gsub(" +", " ", paste0(main, collapse = " "))
   colours_SIR <- expand_SIR_colours(colours_SIR)
 
+  # wildtype/Non-wildtype
+  is_wt_nwt <- identical(breakpoint_type, "ECOFF")
+
   x <- plotrange_as_table(x, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
@@ -824,10 +869,14 @@ plot.disk <- function(x,
   if (any(colours_SIR %in% cols_sub$cols)) {
     legend_txt <- character(0)
     legend_col <- character(0)
-    if (any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
+    if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
       legend_txt <- "(R) Resistant"
       legend_col <- colours_SIR[4]
     }
+    if (is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
+      legend_txt <- "(NWT) Non-wildtype"
+      legend_col <- colours_SIR[4]
+    }
     if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
       legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
       legend_col <- c(legend_col, colours_SIR[3])
@@ -836,10 +885,14 @@ plot.disk <- function(x,
       legend_txt <- c(legend_txt, "(SDD) Susceptible dose-dependent")
       legend_col <- c(legend_col, colours_SIR[2])
     }
-    if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
+    if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
       legend_txt <- c(legend_txt, "(S) Susceptible")
       legend_col <- c(legend_col, colours_SIR[1])
     }
+    if (is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
+      legend_txt <- c(legend_txt, "(WT) Wildtype")
+      legend_col <- c(legend_col, colours_SIR[1])
+    }
     legend("top",
       x.intersp = 0.5,
       legend = translate_into_language(legend_txt, language = language),
@@ -871,6 +924,8 @@ barplot.disk <- function(height,
                          ),
                          language = get_AMR_locale(),
                          expand = TRUE,
+                         include_PKPD = getOption("AMR_include_PKPD", TRUE),
+                         breakpoint_type = getOption("AMR_breakpoint_type", "human"),
                          ...) {
   meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(ylab, allow_class = "character", has_length = 1)
@@ -881,6 +936,8 @@ barplot.disk <- function(height,
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
+  meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
+  meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)
 
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
@@ -893,6 +950,10 @@ barplot.disk <- function(height,
     ab = ab,
     guideline = guideline,
     colours_SIR = colours_SIR,
+    language = language,
+    expand = expand,
+    include_PKPD = include_PKPD,
+    breakpoint_type = breakpoint_type,
     ...
   )
 }
@@ -939,6 +1000,9 @@ autoplot.disk <- function(object,
 
   colours_SIR <- expand_SIR_colours(colours_SIR)
 
+  # wildtype/Non-wildtype
+  is_wt_nwt <- identical(breakpoint_type, "ECOFF")
+
   x <- plotrange_as_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
@@ -956,23 +1020,26 @@ autoplot.disk <- function(object,
   df <- as.data.frame(x, stringsAsFactors = TRUE)
   colnames(df) <- c("disk", "count")
   df$cols <- cols_sub$cols
-  df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
+  df$cols[df$cols == colours_SIR[1] & !is_wt_nwt] <- "(S) Susceptible"
+  df$cols[df$cols == colours_SIR[1] & is_wt_nwt] <- "(WT) Wildtype"
   df$cols[df$cols == colours_SIR[2]] <- "(SDD) Susceptible dose-dependent"
   df$cols[df$cols == colours_SIR[3]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
-  df$cols[df$cols == colours_SIR[4]] <- "(R) Resistant"
+  df$cols[df$cols == colours_SIR[4] & !is_wt_nwt] <- "(R) Resistant"
+  df$cols[df$cols == colours_SIR[4] & is_wt_nwt] <- "(NWT) Non-wildtype"
   df$cols <- factor(translate_into_language(df$cols, language = language),
     levels = translate_into_language(
       c(
         "(S) Susceptible",
         paste("(I)", plot_name_of_I(cols_sub$guideline)),
-        "(R) Resistant"
+        "(R) Resistant",
+        "(WT) Wildtype",
+        "(NWT) Non-wildtype"
       ),
       language = language
     ),
     ordered = TRUE
   )
   p <- ggplot2::ggplot(df)
-
   if (any(colours_SIR %in% cols_sub$cols)) {
     vals <- c(
       "(S) Susceptible" = colours_SIR[1],
@@ -980,7 +1047,9 @@ autoplot.disk <- function(object,
       "(I) Susceptible, incr. exp." = colours_SIR[3],
       "(I) Intermediate" = colours_SIR[3],
       "(R) Resistant" = colours_SIR[4],
-      "(NI) Non-interpretable" = "grey30"
+      "(NI) Non-interpretable" = "grey30",
+      "(WT) Wildtype" = colours_SIR[1],
+      "(NWT) Non-wildtype" = colours_SIR[4]
     )
     names(vals) <- translate_into_language(names(vals), language = language)
     p <- p +
@@ -1028,25 +1097,25 @@ plot.sir <- function(x,
   data <- as.data.frame(table(x), stringsAsFactors = FALSE)
   colnames(data) <- c("x", "n")
   data$s <- round((data$n / sum(data$n)) * 100, 1)
+  data <- data[which(data$n > 0), ]
 
+  if (!all(data$x %in% c("WT", "NWT"), na.rm = TRUE)) {
+    # # be sure to have at least S, I, and R
     if (!"S" %in% data$x) {
       data <- rbind_AMR(data, data.frame(x = "S", n = 0, s = 0, stringsAsFactors = FALSE))
     }
-  if (!"SDD" %in% data$x) {
-    data <- rbind_AMR(data, data.frame(x = "SDD", n = 0, s = 0, stringsAsFactors = FALSE))
-  }
     if (!"I" %in% data$x) {
       data <- rbind_AMR(data, data.frame(x = "I", n = 0, s = 0, stringsAsFactors = FALSE))
     }
     if (!"R" %in% data$x) {
       data <- rbind_AMR(data, data.frame(x = "R", n = 0, s = 0, stringsAsFactors = FALSE))
     }
-  if (!"NI" %in% data$x) {
-    data <- rbind_AMR(data, data.frame(x = "NI", n = 0, s = 0, stringsAsFactors = FALSE))
+    lvls <- VALID_SIR_LEVELS[VALID_SIR_LEVELS %in% c(data$x, c("S", "I", "R"))]
+  } else {
+    lvls <- c("WT", "NWT")
   }
 
-  data <- data[!(data$n == 0 & data$x %in% c("SDD", "I", "NI")), , drop = FALSE]
-  data$x <- factor(data$x, levels = intersect(unique(data$x), c("S", "SDD", "I", "R", "NI")), ordered = TRUE)
+  data$x <- factor(data$x, levels = lvls, ordered = TRUE)
 
   ymax <- pm_if_else(max(data$s) > 95, 105, 100)
 
@@ -1061,7 +1130,7 @@ plot.sir <- function(x,
     axes = FALSE
   )
   # x axis
-  axis(side = 1, at = 1:pm_n_distinct(data$x), labels = levels(data$x), lwd = 0)
+  axis(side = 1, at = seq_along(lvls), labels = lvls, lwd = 0)
   # y axis, 0-100%
   axis(side = 2, at = seq(0, 100, 5))
 
@@ -1104,9 +1173,14 @@ barplot.sir <- function(height,
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
   x <- table(height)
+  if (all(height %in% c("WT", "NWT"), na.rm = TRUE)) {
+    colours_SIR <- colours_SIR[c(1, 4)]
+    x <- x[names(x) %in% c("WT", "NWT")]
+  } else {
     # remove missing I, SDD, and N
     colours_SIR <- colours_SIR[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
     x <- x[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
+  }
   # plot it
   barplot(x,
     col = colours_SIR,
@@ -1152,6 +1226,11 @@ autoplot.sir <- function(object,
   df <- as.data.frame(table(object), stringsAsFactors = TRUE)
   colnames(df) <- c("x", "n")
   df <- df[!(df$n == 0 & df$x %in% c("SDD", "I", "NI")), , drop = FALSE]
+  if (all(object %in% c("WT", "NWT"), na.rm = TRUE)) {
+    df <- df[which(df$x %in% c("WT", "NWT")), ]
+  } else {
+    df <- df[which(!df$x %in% c("WT", "NWT", "NS")), ]
+  }
   ggplot2::ggplot(df) +
     ggplot2::geom_col(ggplot2::aes(x = x, y = n, fill = x)) +
     # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
@@ -1161,7 +1240,9 @@ autoplot.sir <- function(object,
         "SDD" = colours_SIR[2],
         "I" = colours_SIR[3],
         "R" = colours_SIR[4],
-        "NI" = "grey30"
+        "NI" = "grey30",
+        "WT" = colours_SIR[1],
+        "NWT" = colours_SIR[4]
       ),
       limits = force
     ) +
@@ -1290,6 +1371,9 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f
     cols[sir == "I"] <- colours_SIR[3]
     cols[sir == "R"] <- colours_SIR[4]
     cols[sir == "NI"] <- "grey30"
+    cols[sir == "WT"] <- colours_SIR[1]
+    cols[sir == "NWT"] <- colours_SIR[4]
+    cols[sir == "NS"] <- colours_SIR[4]
     sub <- bquote(.(abname) ~ "-" ~ italic(.(moname)) ~ .(guideline_txt))
   } else {
     cols <- "#BEBEBE"

R/proportion.R

@@ -38,6 +38,11 @@
 #' @param only_all_tested (for combination therapies, i.e. using more than one variable for `...`): a [logical] to indicate that isolates must be tested for all antimicrobials, see section *Combination Therapy* below.
 #' @param data A [data.frame] containing columns with class [`sir`] (see [as.sir()]).
 #' @param translate_ab A column name of the [antimicrobials] data set to translate the antibiotic abbreviations to, using [ab_property()].
+#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
+#'   * EUCAST: [susceptibility()] \eqn{= \%S + \%I}, [resistance()] \eqn{= \%R}
+#'   * CLSI: [susceptibility()] \eqn{= \%S + \%SDD}, [resistance()] \eqn{= \%I + \%R}
+#'
+#' You can also use e.g. [proportion_R()] or [proportion_S()] instead, to be explicit.
 #' @inheritParams ab_property
 #' @param combine_SI A [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is `TRUE`.
 #' @param ab_result Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".
@@ -228,10 +233,20 @@
 resistance <- function(...,
                        minimum = 30,
                        as_percent = FALSE,
-                       only_all_tested = FALSE) {
+                       only_all_tested = FALSE,
+                       guideline = getOption("AMR_guideline", "EUCAST")) {
+  # other arguments for meet_criteria are handled by sir_calc()
+  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
+    message_("`resistance()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("This message will be shown once per session.")
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = "R",
+      ab_result = c(
+        "R", "NWT", "NS",
+        if (identical(guideline, "CLSI")) "I"
+      ),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -246,10 +261,20 @@ resistance <- function(...,
 susceptibility <- function(...,
                            minimum = 30,
                            as_percent = FALSE,
-                           only_all_tested = FALSE) {
+                           only_all_tested = FALSE,
+                           guideline = getOption("AMR_guideline", "EUCAST")) {
+  # other arguments for meet_criteria are handled by sir_calc()
+  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
+    message_("`susceptibility()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("This message will be shown once per session.")
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "SDD", "I"),
+      ab_result = c(
+        "S", "SDD", "WT",
+        if (identical(guideline, "EUCAST")) "I"
+      ),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -269,7 +294,7 @@ sir_confidence_interval <- function(...,
                                     confidence_level = 0.95,
                                     side = "both",
                                     collapse = FALSE) {
-  meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = c(1:5), is_in = c("S", "SDD", "I", "R", "NI"))
+  meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = seq_along(VALID_SIR_LEVELS), is_in = VALID_SIR_LEVELS)
   meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
   meet_criteria(as_percent, allow_class = "logical", has_length = 1)
   meet_criteria(only_all_tested, allow_class = "logical", has_length = 1)
@@ -287,7 +312,7 @@ sir_confidence_interval <- function(...,
   )
   n <- tryCatch(
     sir_calc(...,
-      ab_result = c("S", "SDD", "I", "R", "NI"),
+      ab_result = VALID_SIR_LEVELS,
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -341,7 +366,7 @@ proportion_R <- function(...,
                          only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = "R",
+      ab_result = c("R", "NWT", "NS"),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -359,7 +384,7 @@ proportion_IR <- function(...,
                           only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = c("I", "SDD", "R"),
+      ab_result = c("I", "SDD", "R", "NWT", "NS"),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -395,7 +420,7 @@ proportion_SI <- function(...,
                           only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "I", "SDD"),
+      ab_result = c("S", "I", "SDD", "WT"),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -413,7 +438,7 @@ proportion_S <- function(...,
                          only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = "S",
+      ab_result = c("S", "WT"),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,

R/sir.R

@@ -27,6 +27,8 @@
 # how to conduct AMR data analysis: https://amr-for-r.org              #
 # ==================================================================== #
 
+VALID_SIR_LEVELS <- c("S", "SDD", "I", "R", "NI", "WT", "NWT", "NS")
+
 #' Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
 #'
 #' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor] containing the levels `S`, `SDD`, `I`, `R`, `NI`.
@@ -42,22 +44,23 @@
 #' @param capped_mic_handling A [character] string that controls how MIC values with a cap (i.e., starting with `<`, `<=`, `>`, or `>=`) are interpreted. Supports the following options:
 #'
 #' `"none"`
-#'   * `<=` and `>=` are treated as-is.
-#'   * `<` and `>` are treated as-is.
+#'   * `<=`, `<`, `>` and `>=` are ignored.
 #'
-#' `"conservative"`
-#'   * `<=` and `>=` return `"NI"` (non-interpretable) if the MIC is within the breakpoint guideline range.
-#'   * `<` always returns `"S"`, and `>` always returns `"R"`.
+#' `"conservative"` (default)
+#'   * `<=`, `<`, `>` and `>=` return `"NI"` (non-interpretable) if the *true* MIC could be at either side of the breakpoint.
+#'   * This is the only mode that preserves uncertainty for ECOFFs.
 #'
-#' `"standard"` (default)
-#'   * `<=` and `>=` return `"NI"` (non-interpretable) if the MIC is within the breakpoint guideline range.
-#'   * `<` and `>` are treated as-is.
+#' `"standard"`
+#'   * `<=` and `>=` return `"NI"` (non-interpretable) if the *true* MIC could be at either side of the breakpoint.
+#'   * `<` always returns `"S"`, regardless of the breakpoint.
+#'   * `>` always returns `"R"`, regardless of the breakpoint.
 #'
-#' `"inverse"`
-#'   * `<=` and `>=` are treated as-is.
-#'   * `<` always returns `"S"`, and `>` always returns `"R"`.
+#' `"lenient"`
+#'   * `<=` and `<` always return `"S"`, regardless of the breakpoint.
+#'   * `>=` and `>` always return `"R"`, regardless of the breakpoint.
 #'
-#' The default `"standard"` setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option [`AMR_capped_mic_handling`][AMR-options].
+#' The default `"conservative"` setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option [`AMR_capped_mic_handling`][AMR-options].
+#' @param as_wt_nwt A [logical] to return `"WT"`/`"NWT"` instead of `"S"`/`"R"`. Defaults to `TRUE` when using ECOFFs, i.e., when `breakpoint_type` is set to `"ECOFF"`.
 #' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
 #' @param substitute_missing_r_breakpoint A [logical] to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is `FALSE`. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning that the outcome can only be `"S"` or `NA`. Setting this to `TRUE` will convert the `NA`s in these cases to `"R"`. Can also be set with the package option [`AMR_substitute_missing_r_breakpoint`][AMR-options].
 #' @param include_screening A [logical] to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`. Can also be set with the package option [`AMR_include_screening`][AMR-options].
@@ -69,7 +72,7 @@
 #' @param reference_data A [data.frame] to be used for interpretation, which defaults to the [clinical_breakpoints] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [clinical_breakpoints] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
 #' @param threshold Maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*.
 #' @param conserve_capped_values Deprecated, use `capped_mic_handling` instead.
-#' @param ... For using on a [data.frame]: selection of columns to apply `as.sir()` to. Supports [tidyselect language][tidyselect::starts_with()] such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and can thus also be [antimicrobial selectors][amr_selector()] such as `as.sir(df, penicillins())`.
+#' @param ... For using on a [data.frame]: selection of columns to apply `as.sir()` to. Supports [tidyselect language][tidyselect::starts_with()] such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and can thus also be [antimicrobial selectors][amr_selector()], e.g. `as.sir(df, penicillins())`.
 #'
 #' Otherwise: arguments passed on to methods.
 #' @details
@@ -95,7 +98,7 @@
 #'      # fast processing with parallel computing:
 #'      as.sir(your_data, ..., parallel = TRUE)
 #'      ```
-#'    * Operators like "<=" will be stripped before interpretation. When using `capped_mic_handling = "conservative"`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`capped_mic_handling = "standard"`) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
+#'    * Operators like "<=" will be considered according to the `capped_mic_handling` setting. At default, an MIC value of e.g. ">2" will return "NI" (non-interpretable) if the breakpoint is 4-8; the *true* MIC could be at either side of the breakpoint. This is to prevent that capped values from raw laboratory data would not be treated conservatively.
 #'    * **Note:** When using CLSI as the guideline, MIC values must be log2-based doubling dilutions. Values not in this format, will be automatically rounded up to the nearest log2 level as CLSI instructs, and a warning will be thrown.
 #'
 #' 3. For **interpreting disk diffusion diameters** according to EUCAST or CLSI. You must clean your disk zones first using [as.disk()], that also gives your columns the new data class [`disk`]. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the `mo` argument.
@@ -153,9 +156,9 @@
 #'
 #' ### After Interpretation
 #'
-#' After using [as.sir()], you can use the [eucast_rules()] defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
+#' After using [as.sir()], you can use the [interpretive_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
 #'
-#' To determine which isolates are multi-drug resistant, be sure to run [mdro()] (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about [interpreting multidrug-resistant organisms here][mdro()].
+#' To determine which isolates are multi-drug resistant, be sure to run [mdro()] (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about [detecting multidrug-resistant organisms here][mdro()].
 #'
 #' ### Other
 #'
@@ -165,7 +168,7 @@
 #'
 #' The function [is_sir_eligible()] returns `TRUE` when a column contains at most 5% potentially invalid antimicrobial interpretations, and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector.
 #' @section Interpretation of SIR:
-#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<https://www.eucast.org/newsiandr>).
+#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
 #'
 #' This AMR package follows insight; use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
 #' @return Ordered [factor] with new class `sir`
@@ -179,7 +182,7 @@
 #' - **CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/microbiology/documents/m100/>.
 #' - **CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.
 ###### TODO  - **CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet09/>.
-#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/clinical_breakpoints>.
+#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
 #' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. <https://whonet.org/>.
 #'
 #' @inheritSection AMR Download Our Reference Data
@@ -353,6 +356,10 @@
 #'
 #' as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
 #' as.sir("<= 0.002; S") # will return "S"
+#'
+#' as.sir(c(1, 2, 3))
+#' as.sir(c(1, 2, 3), S = 3, I = 2, R = 1)
+#'
 #' sir_data <- as.sir(c(rep("S", 474), rep("I", 36), rep("R", 370)))
 #' is.sir(sir_data)
 #' plot(sir_data) # for percentages
@@ -394,7 +401,7 @@ as_sir_structure <- function(x,
                              ref_breakpoints = NULL) {
   structure(
     factor(as.character(unlist(unname(x))),
-      levels = c("S", "SDD", "I", "R", "NI"),
+      levels = VALID_SIR_LEVELS,
       ordered = TRUE
     ),
     # TODO for #170
@@ -450,9 +457,9 @@ is_sir_eligible <- function(x, threshold = 0.05) {
   %in% class(x))) {
     # no transformation needed
     return(FALSE)
-  } else if (!all(is.na(x)) && all(x %in% c("S", "SDD", "I", "R", "NI", NA, "s", "sdd", "i", "r", "ni"))) {
+  } else if (!all(is.na(x)) && all(x %in% c(VALID_SIR_LEVELS, tolower(VALID_SIR_LEVELS), NA))) {
     return(TRUE)
-  } else if (!all(is.na(x)) && !any(c("S", "SDD", "I", "R", "NI") %in% gsub("([SIR])\\1+", "\\1", gsub("[^A-Z]", "", toupper(unique(x[1:10000])), perl = TRUE), perl = TRUE), na.rm = TRUE)) {
+  } else if (!all(is.na(x)) && !any(VALID_SIR_LEVELS %in% gsub("([SIR])\\1+", "\\1", gsub("[^A-Z]", "", toupper(unique(x[1:10000])), perl = TRUE), perl = TRUE), na.rm = TRUE)) {
     return(FALSE)
   } else {
     x <- x[!is.na(x) & !is.null(x) & !x %in% c("", "-", "NULL")]
@@ -482,22 +489,28 @@ is_sir_eligible <- function(x, threshold = 0.05) {
 
 #' @rdname as.sir
 #' @export
-#' @param S,I,R,NI,SDD A case-independent [regular expression][base::regex] to translate input to this result. This regular expression will be run *after* all non-letters and whitespaces are removed from the input.
+#' @param S,I,R,NI,SDD,WT,NWT,NS A case-independent [regular expression][base::regex] to translate input to this result. This regular expression will be run *after* all non-letters and whitespaces are removed from the input.
 #' @param info A [logical] to print information about the process, defaults to `TRUE` only in [interactive sessions][base::interactive()].
 # extra param: warn (logical, to never throw a warning)
 as.sir.default <- function(x,
-                           S = "^(S|U)+$",
-                           I = "^(I)+$",
-                           R = "^(R)+$",
-                           NI = "^(N|NI|V)+$",
-                           SDD = "^(SDD|D|H)+$",
+                           S = "^(S|U|1)+$",
+                           I = "^(I|2)+$",
+                           R = "^(R|3)+$",
+                           NI = "^(N|NI|V|4)+$",
+                           SDD = "^(SDD|D|H|5)+$",
+                           WT = "^(WT|6)+$",
+                           NWT = "^(NWT|7)+$",
+                           NS = "^(NS|8)+$",
                            info = interactive(),
                            ...) {
-  meet_criteria(S, allow_class = "character", has_length = 1)
-  meet_criteria(I, allow_class = "character", has_length = 1)
-  meet_criteria(R, allow_class = "character", has_length = 1)
-  meet_criteria(NI, allow_class = "character", has_length = 1)
-  meet_criteria(SDD, allow_class = "character", has_length = 1)
+  meet_criteria(S, allow_class = c("character", "numeric", "integer", "factor"), has_length = 1)
+  meet_criteria(I, allow_class = c("character", "numeric", "integer", "factor"), has_length = 1)
+  meet_criteria(R, allow_class = c("character", "numeric", "integer", "factor"), has_length = 1)
+  meet_criteria(NI, allow_class = c("character", "numeric", "integer", "factor"), has_length = 1)
+  meet_criteria(SDD, allow_class = c("character", "numeric", "integer", "factor"), has_length = 1)
+  meet_criteria(WT, allow_class = c("character", "numeric", "integer", "factor"), has_length = 1)
+  meet_criteria(NWT, allow_class = c("character", "numeric", "integer", "factor"), has_length = 1)
+  meet_criteria(NS, allow_class = c("character", "numeric", "integer", "factor"), has_length = 1)
   meet_criteria(info, allow_class = "logical", has_length = 1)
   if (inherits(x, "sir")) {
     return(as_sir_structure(x))
@@ -506,30 +519,14 @@ as.sir.default <- function(x,
   x.bak <- x
   x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
 
-  if (inherits(x.bak, c("numeric", "integer")) && all(x %in% c(1:3, NA))) {
+  lbls <- attr(x.bak, "labels", exact = TRUE)
+  if (inherits(x.bak, c("numeric", "integer")) && all(x %in% c(1:3, NA)) && !is.null(lbls) && all(c("S", "I", "R") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
     # support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
-    lbls <- attributes(x.bak)$labels
-    if (!is.null(lbls) && all(c("S", "I", "R") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
     x[x.bak == 1] <- names(lbls[lbls == 1])
     x[x.bak == 2] <- names(lbls[lbls == 2])
     x[x.bak == 3] <- names(lbls[lbls == 3])
-    } else {
-      x[x.bak == 1] <- "S"
-      x[x.bak == 2] <- "I"
-      x[x.bak == 3] <- "R"
-    }
-  } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "I", "R", NA_character_))) {
-    x[x.bak == "1"] <- "S"
-    x[x.bak == "2"] <- "I"
-    x[x.bak == "3"] <- "R"
-  } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "4", "5", "S", "SDD", "I", "R", "NI", NA_character_))) {
-    x[x.bak == "1"] <- "S"
-    x[x.bak == "2"] <- "SDD"
-    x[x.bak == "3"] <- "I"
-    x[x.bak == "4"] <- "R"
-    x[x.bak == "5"] <- "NI"
-  } else if (!all(is.na(x)) && !identical(levels(x), c("S", "SDD", "I", "R", "NI")) && !all(x %in% c("S", "SDD", "I", "R", "NI", NA))) {
-    if (all(x %unlike% "(S|I|R)", na.rm = TRUE)) {
+  } else if (!all(is.na(x)) && !identical(levels(x), VALID_SIR_LEVELS) && !all(x %in% c(VALID_SIR_LEVELS, NA))) {
+    if (all(x %unlike% "(S|I|R)", na.rm = TRUE) && !all(x %in% c(1, 2, 3, 4, 5), na.rm = TRUE)) {
       # check if they are actually MICs or disks
       if (all_valid_mics(x)) {
         warning_("in `as.sir()`: input values were guessed to be MIC values - preferably transform them with `as.mic()` before running `as.sir()`.")
@@ -569,17 +566,43 @@ as.sir.default <- function(x,
     x[x %like% "not|non"] <- "NI"
     x[x %like% "([^a-z]|^)int(er(mediate)?)?|incr.*exp"] <- "I"
     x[x %like% "dose"] <- "SDD"
-    x <- gsub("[^A-Z]+", "", x, perl = TRUE)
+    mtch <- grepl(paste0("(", S, "|", I, "|", R, "|", NI, "|", SDD, "|", WT, "|", NWT, "|", NS, "|[A-Z]+)"), x, perl = TRUE)
+    x[!mtch] <- ""
     # apply regexes set by user
     x[x %like% S] <- "S"
     x[x %like% I] <- "I"
     x[x %like% R] <- "R"
     x[x %like% NI] <- "NI"
     x[x %like% SDD] <- "SDD"
-    x[!x %in% c("S", "SDD", "I", "R", "NI")] <- NA_character_
+    x[x %like% WT] <- "WT"
+    x[x %like% NWT] <- "NWT"
+    x[x %like% NS] <- "NS"
+    x[!x %in% VALID_SIR_LEVELS] <- NA_character_
     na_after <- length(x[is.na(x) | x == ""])
 
     if (!isFALSE(list(...)$warn)) { # so as.sir(..., warn = FALSE) will never throw a warning
+      if (all(x.bak %in% c(1:8), na.rm = TRUE) && message_not_thrown_before("as.sir", "numeric_interpretation", x, x.bak)) {
+        out1 <- unique(x[x.bak == 1])
+        out2 <- unique(x[x.bak == 2])
+        out3 <- unique(x[x.bak == 3])
+        out4 <- unique(x[x.bak == 4])
+        out5 <- unique(x[x.bak == 5])
+        out6 <- unique(x[x.bak == 6])
+        out7 <- unique(x[x.bak == 7])
+        out8 <- unique(x[x.bak == 8])
+        out <- c(
+          ifelse(length(out1) > 0, paste0("1 as \"", out1, "\""), NA_character_),
+          ifelse(length(out2) > 0, paste0("2 as \"", out2, "\""), NA_character_),
+          ifelse(length(out3) > 0, paste0("3 as \"", out3, "\""), NA_character_),
+          ifelse(length(out4) > 0, paste0("4 as \"", out4, "\""), NA_character_),
+          ifelse(length(out5) > 0, paste0("5 as \"", out5, "\""), NA_character_),
+          ifelse(length(out6) > 0, paste0("6 as \"", out6, "\""), NA_character_),
+          ifelse(length(out7) > 0, paste0("7 as \"", out7, "\""), NA_character_),
+          ifelse(length(out8) > 0, paste0("8 as \"", out8, "\""), NA_character_)
+        )
+        message_("in `as.sir()`: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
+      }
+
       if (na_before != na_after) {
         list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
           unique() %pm>%
@@ -588,7 +611,7 @@ as.sir.default <- function(x,
         cur_col <- get_current_column()
         warning_("in `as.sir()`: ", na_after - na_before, " result",
           ifelse(na_after - na_before > 1, "s", ""),
-          ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
+          ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
           " truncated (",
           round(((na_after - na_before) / length(x)) * 100),
           "%) that were invalid antimicrobial interpretations: ",
@@ -610,6 +633,7 @@ as.sir.mic <- function(x,
                        guideline = getOption("AMR_guideline", "EUCAST"),
                        uti = NULL,
                        capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
+                       as_wt_nwt = identical(breakpoint_type, "ECOFF"),
                        add_intrinsic_resistance = FALSE,
                        reference_data = AMR::clinical_breakpoints,
                        substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
@@ -631,6 +655,7 @@ as.sir.mic <- function(x,
     guideline = guideline,
     uti = uti,
     capped_mic_handling = capped_mic_handling,
+    as_wt_nwt = as_wt_nwt,
     add_intrinsic_resistance = add_intrinsic_resistance,
     reference_data = reference_data,
     substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
@@ -653,6 +678,7 @@ as.sir.disk <- function(x,
                         ab = deparse(substitute(x)),
                         guideline = getOption("AMR_guideline", "EUCAST"),
                         uti = NULL,
+                        as_wt_nwt = identical(breakpoint_type, "ECOFF"),
                         add_intrinsic_resistance = FALSE,
                         reference_data = AMR::clinical_breakpoints,
                         substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
@@ -673,6 +699,7 @@ as.sir.disk <- function(x,
     guideline = guideline,
     uti = uti,
     capped_mic_handling = "standard", # will be ignored for non-MIC anyway
+    as_wt_nwt = as_wt_nwt,
     add_intrinsic_resistance = add_intrinsic_resistance,
     reference_data = reference_data,
     substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
@@ -697,6 +724,7 @@ as.sir.data.frame <- function(x,
                               guideline = getOption("AMR_guideline", "EUCAST"),
                               uti = NULL,
                               capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
+                              as_wt_nwt = identical(breakpoint_type, "ECOFF"),
                               add_intrinsic_resistance = FALSE,
                               reference_data = AMR::clinical_breakpoints,
                               substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
@@ -714,7 +742,8 @@ as.sir.data.frame <- function(x,
   meet_criteria(col_mo, allow_class = "character", is_in = colnames(x), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character")
   meet_criteria(uti, allow_class = c("logical", "character"), allow_NULL = TRUE, allow_NA = TRUE)
-  meet_criteria(capped_mic_handling, allow_class = "character", has_length = 1, is_in = c("standard", "conservative", "none", "inverse"))
+  meet_criteria(capped_mic_handling, allow_class = "character", has_length = 1, is_in = c("none", "conservative", "standard", "lenient"))
+  meet_criteria(as_wt_nwt, allow_class = "logical", has_length = 1)
   meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
   meet_criteria(reference_data, allow_class = "data.frame")
   meet_criteria(substitute_missing_r_breakpoint, allow_class = "logical", has_length = 1)
@@ -795,8 +824,8 @@ as.sir.data.frame <- function(x,
     col_specimen <- suppressMessages(search_type_in_df(x = x, type = "specimen", info = info))
     if (!is.null(col_specimen)) {
       uti <- x[, col_specimen, drop = TRUE] %like% "urin"
-      values <- sort(unique(x[uti, col_specimen, drop = TRUE]))
-      if (length(values) > 1) {
+      col_values <- sort(unique(x[uti, col_specimen, drop = TRUE]))
+      if (length(col_values) > 1) {
         plural <- c("s", "", "")
       } else {
         plural <- c("", "s", "a ")
@@ -804,7 +833,7 @@ as.sir.data.frame <- function(x,
       if (isTRUE(info)) {
         message_(
           "Assuming value", plural[1], " ",
-          vector_and(values, quotes = TRUE),
+          vector_and(col_values, quotes = TRUE),
           " in column '", font_bold(col_specimen),
           "' reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
           ".\n  Use `as.sir(uti = FALSE)` to prevent this."
@@ -894,6 +923,7 @@ as.sir.data.frame <- function(x,
           guideline = guideline,
           uti = uti,
           capped_mic_handling = capped_mic_handling,
+          as_wt_nwt = as_wt_nwt,
           add_intrinsic_resistance = add_intrinsic_resistance,
           reference_data = reference_data,
           substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
@@ -921,6 +951,7 @@ as.sir.data.frame <- function(x,
           ab = ab_col,
           guideline = guideline,
           uti = uti,
+          as_wt_nwt = as_wt_nwt,
           add_intrinsic_resistance = add_intrinsic_resistance,
           reference_data = reference_data,
           substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
@@ -983,7 +1014,7 @@ as.sir.data.frame <- function(x,
       on.exit(parallel::stopCluster(cl), add = TRUE)
       parallel::clusterExport(cl, varlist = c(
         "x", "x.bak", "x_mo", "ab_cols", "types",
-        "capped_mic_handling", "add_intrinsic_resistance",
+        "capped_mic_handling", "as_wt_nwt", "add_intrinsic_resistance",
         "reference_data", "substitute_missing_r_breakpoint", "include_screening", "include_PKPD",
         "breakpoint_type", "guideline", "host", "uti", "info", "verbose",
         "col_mo", "AMR_env", "conserve_capped_values",
@@ -1096,6 +1127,7 @@ as_sir_method <- function(method_short,
                           guideline,
                           uti,
                           capped_mic_handling,
+                          as_wt_nwt,
                           add_intrinsic_resistance,
                           reference_data,
                           substitute_missing_r_breakpoint,
@@ -1117,7 +1149,8 @@ as_sir_method <- function(method_short,
   meet_criteria(ab, allow_class = c("ab", "character"), has_length = c(1, length(x)), .call_depth = -2)
   meet_criteria(guideline, allow_class = "character", has_length = c(1, length(x)), .call_depth = -2)
   meet_criteria(uti, allow_class = c("logical", "character"), has_length = c(1, length(x)), allow_NULL = TRUE, allow_NA = TRUE, .call_depth = -2)
-  meet_criteria(capped_mic_handling, allow_class = "character", has_length = 1, is_in = c("standard", "conservative", "none", "inverse"), .call_depth = -2)
+  meet_criteria(capped_mic_handling, allow_class = "character", has_length = 1, is_in = c("none", "conservative", "standard", "lenient"), .call_depth = -2)
+  meet_criteria(as_wt_nwt, allow_class = "logical", has_length = 1, .call_depth = -2)
   meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1, .call_depth = -2)
   meet_criteria(reference_data, allow_class = "data.frame", .call_depth = -2)
   meet_criteria(substitute_missing_r_breakpoint, allow_class = "logical", has_length = 1, .call_depth = -2)
@@ -1378,8 +1411,8 @@ as_sir_method <- function(method_short,
 
   # create the unique data frame to be filled to save time
   df <- data.frame(
-    values = x,
-    values_bak = x,
+    input_clean = x,
+    input_original = x,
     guideline = guideline_coerced,
     mo = mo,
     ab = ab,
@@ -1393,7 +1426,7 @@ as_sir_method <- function(method_short,
       # CLSI in log 2 ----
       # CLSI says: if MIC is not a log2 value it must be rounded up to the nearest log2 value
       log2_levels <- as.double(VALID_MIC_LEVELS[which(VALID_MIC_LEVELS %in% 2^c(-20:20))])
-      test_values <- df$values
+      test_values <- df$input_clean
       test_values_dbl <- as.double(test_values)
       test_values_dbl[test_values %like% "^>[0-9]"] <- test_values_dbl[test_values %like% "^>[0-9]"] + 0.0000001
       test_values_dbl[test_values %like% "^<[0-9]"] <- test_values_dbl[test_values %like% "^<[0-9]"] - 0.0000001
@@ -1404,8 +1437,7 @@ as_sir_method <- function(method_short,
           if (is.na(mic_val)) {
             return(NA_real_)
           } else {
-            # find the smallest log2 level that is >= mic_val
-            log2_val <- log2_levels[which(log2_levels >= as.double(mic_val))][1]
+            log2_val <- COMMON_MIC_VALUES[which(COMMON_MIC_VALUES >= as.double(mic_val))][1]
             if (!is.na(log2_val) && as.double(mic_val) != log2_val) {
               if (message_not_thrown_before("as.sir", "CLSI", "MICupscaling")) {
                 warning_("Some MICs were converted to the nearest higher log2 level, following the CLSI interpretation guideline.")
@@ -1417,12 +1449,12 @@ as_sir_method <- function(method_short,
           }
         }
       )
-      df$values[which(df$guideline %like% "CLSI" & test_values != test_outcome)] <- test_outcome[which(df$guideline %like% "CLSI" & test_values != test_outcome)]
+      df$input_clean[which(df$guideline %like% "CLSI" & test_values != test_outcome)] <- test_outcome[which(df$guideline %like% "CLSI" & test_values != test_outcome)]
     }
-    df$values <- as.mic(df$values)
+    df$input_clean <- as.mic(df$input_clean)
   } else if (method == "disk") {
     # when as.sir.disk is called directly
-    df$values <- as.disk(df$values)
+    df$input_clean <- as.disk(df$input_clean)
   }
 
   df_unique <- unique(df[, c("guideline", "mo", "ab", "uti", "host"), drop = FALSE])
@@ -1500,8 +1532,8 @@ as_sir_method <- function(method_short,
       # this can happen if a host is unavailable, just continue with the next one, since a note about hosts having NA are already given at this point
       next
     }
-    values <- df[rows, "values", drop = TRUE]
-    values_bak <- df[rows, "values_bak", drop = TRUE]
+    input_clean <- df[rows, "input_clean", drop = TRUE]
+    input_original <- df[rows, "input_original", drop = TRUE]
     notes_current <- rep("", length(rows))
     new_sir <- rep(NA_sir_, length(rows))
 
@@ -1636,11 +1668,11 @@ as_sir_method <- function(method_short,
         ab_given = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
         mo_given = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
         host_given = vectorise_log_entry(host.bak[match(host_current, df$host)][1], length(rows)),
-        input_given = vectorise_log_entry(as.character(values_bak), length(rows)),
+        input_given = vectorise_log_entry(as.character(input_original), length(rows)),
         ab = vectorise_log_entry(ab_current, length(rows)),
         mo = vectorise_log_entry(mo_current, length(rows)),
         host = vectorise_log_entry(host_current, length(rows)),
-        input = vectorise_log_entry(as.character(values), length(rows)),
+        input = vectorise_log_entry(as.character(input_clean), length(rows)),
         outcome = vectorise_log_entry(NA_sir_, length(rows)),
         notes = vectorise_log_entry("No breakpoint available", length(rows)),
         guideline = vectorise_log_entry(guideline_current, length(rows)),
@@ -1734,31 +1766,51 @@ as_sir_method <- function(method_short,
           ""
         ),
         "\n",
-        ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[<][0-9]",
-          paste0("MIC values with the operator '<' are all considered 'S' since capped_mic_handling = \"", capped_mic_handling, "\"."),
+        ifelse(method == "mic" & capped_mic_handling == "none" & as.character(input_original) %like% "^[<>][0-9]" &
+          ((as.character(input_original) %like% "^<" & as.double(input_clean) > breakpoints_current$breakpoint_S) |
+            (as.character(input_original) %like% "^>" & as.double(input_clean) < breakpoints_current$breakpoint_R)),
+        paste0("Operators such as '<' and '>' were ignored since capped_mic_handling = \"", capped_mic_handling, "\"."),
         ""
         ),
         "\n",
-        ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[>][0-9]",
-          paste0("MIC values with the operator '>' are all considered 'R' since capped_mic_handling = \"", capped_mic_handling, "\"."),
+        ifelse(method == "mic" & capped_mic_handling == "standard" & as.character(input_original) %like% "^[<][0-9]",
+          paste0("MIC values with the operator '<' are considered 'S' since capped_mic_handling = \"", capped_mic_handling, "\"."),
           ""
         ),
         "\n",
-        ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^[><]=[0-9]" & as.double(values) > breakpoints_current$breakpoint_S & as.double(values) < breakpoints_current$breakpoint_R,
-          paste0("MIC values within the breakpoint guideline range with the operator '<=' or '>=' are considered 'NI' (non-interpretable) since capped_mic_handling = \"", capped_mic_handling, "\"."),
+        ifelse(method == "mic" & capped_mic_handling == "standard" & as.character(input_original) %like% "^[>][0-9]",
+          paste0("MIC values with the operator '>' are considered 'R' since capped_mic_handling = \"", capped_mic_handling, "\"."),
           ""
         ),
         "\n",
-        ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^<=[0-9]" & as.double(values) == breakpoints_current$breakpoint_R,
-          paste0("MIC values at the R breakpoint with the operator '<=' are considered 'NI' (non-interpretable) since capped_mic_handling = \"", capped_mic_handling, "\"."),
+        ifelse(method == "mic" & capped_mic_handling == "lenient" & as.character(input_original) %like% "^[<]=?[0-9]",
+          paste0("MIC values with the operator '<' or '<=' are considered 'S' since capped_mic_handling = \"", capped_mic_handling, "\"."),
           ""
         ),
         "\n",
-        ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^>=[0-9]" & as.double(values) == breakpoints_current$breakpoint_S,
-          paste0("MIC values at the S breakpoint with the operator '>=' are considered 'NI' (non-interpretable) since capped_mic_handling = \"", capped_mic_handling, "\"."),
+        ifelse(method == "mic" & capped_mic_handling == "lenient" & as.character(input_original) %like% "^[>]=?[0-9]",
+          paste0("MIC values with the operator '>' or '>=' are considered 'R' since capped_mic_handling = \"", capped_mic_handling, "\"."),
+          ""
+        ),
+        "\n",
+        ifelse(method == "mic" & capped_mic_handling == "conservative" & as.character(input_original) %like% "^[<>][0-9]" &
+          ((as.character(input_original) %like% "^<" & as.double(input_clean) > breakpoints_current$breakpoint_S) |
+            (as.character(input_original) %like% "^>" & as.double(input_clean) < breakpoints_current$breakpoint_R)),
+        paste0("MIC values are considered 'NI' (non-interpretable) if the true MIC could be at either side of the breakpoint and capped_mic_handling = \"", capped_mic_handling, "\"."),
+        ""
+        ),
+        "\n",
+        ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "standard") & as.character(input_original) %like% "^<=[0-9]" & as.double(input_clean) > breakpoints_current$breakpoint_S,
+          paste0("MIC values are considered 'NI' (non-interpretable) if the true MIC could be at either side of the breakpoint and capped_mic_handling = \"", capped_mic_handling, "\"."),
+          ""
+        ),
+        "\n",
+        ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "standard") & as.character(input_original) %like% "^>=[0-9]" & as.double(input_clean) <= breakpoints_current$breakpoint_R,
+          paste0("MIC values are considered 'NI' (non-interpretable) if the true MIC could be at either side of the breakpoint and capped_mic_handling = \"", capped_mic_handling, "\"."),
           ""
         )
       )
+
       if (isTRUE(substitute_missing_r_breakpoint) && !is.na(breakpoints_current$breakpoint_S) && is.na(breakpoints_current$breakpoint_R)) {
         # breakpoints_current only has 1 row at this moment
         breakpoints_current$breakpoint_R <- breakpoints_current$breakpoint_S
@@ -1774,27 +1826,62 @@ as_sir_method <- function(method_short,
       ## actual interpretation ----
       if (method == "mic") {
         new_sir <- case_when_AMR(
-          is.na(values) ~ NA_sir_,
-          capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[<][0-9]" ~ as.sir("S"),
-          capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[>][0-9]" ~ as.sir("R"),
-          capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^[><]=[0-9]" & as.double(values) > breakpoints_current$breakpoint_S & as.double(values) < breakpoints_current$breakpoint_R ~ as.sir("NI"),
-          capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^<=[0-9]" & as.double(values) == breakpoints_current$breakpoint_R ~ as.sir("NI"),
-          capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^>=[0-9]" & as.double(values) == breakpoints_current$breakpoint_S ~ as.sir("NI"),
-          values <= breakpoints_current$breakpoint_S ~ as.sir("S"),
-          guideline_current %like% "EUCAST" & values > breakpoints_current$breakpoint_R ~ as.sir("R"),
-          guideline_current %like% "CLSI" & values >= breakpoints_current$breakpoint_R ~ as.sir("R"),
+          is.na(input_clean) ~ NA_sir_,
+
+          # "lenient" for any cap: force S/R
+          capped_mic_handling == "lenient" &
+            as.character(input_original) %like% "^[<]=?[0-9]"
+          ~ as.sir("S"),
+          capped_mic_handling == "lenient" &
+            as.character(input_original) %like% "^[>]=?[0-9]"
+          ~ as.sir("R"),
+
+          # "standard" for < and >: force S/R
+          capped_mic_handling == "standard" &
+            as.character(input_original) %like% "^[<][0-9]"
+          ~ as.sir("S"),
+          capped_mic_handling == "standard" &
+            as.character(input_original) %like% "^[>][0-9]"
+          ~ as.sir("R"),
+
+          # "conservative" for < and >: NI if the true MIC could be on either side of a breakpoint
+          capped_mic_handling == "conservative" &
+            as.character(input_original) %like% "^[<][0-9]" &
+            as.double(input_clean) > breakpoints_current$breakpoint_S
+          ~ as.sir("NI"),
+          capped_mic_handling == "conservative" &
+            as.character(input_original) %like% "^[>][0-9]" &
+            as.double(input_clean) < breakpoints_current$breakpoint_R
+          ~ as.sir("NI"),
+
+          # both "conservative" and standard": only NI for <= and >= when the true MIC could be at either side of a breakpoint
+          capped_mic_handling %in% c("conservative", "standard") &
+            as.character(input_original) %like% "^<=[0-9]" &
+            as.double(input_clean) > breakpoints_current$breakpoint_S
+          ~ as.sir("NI"),
+          capped_mic_handling %in% c("conservative", "standard") &
+            as.character(input_original) %like% "^>=[0-9]" &
+            as.double(input_clean) <= breakpoints_current$breakpoint_R
+          ~ as.sir("NI"),
+
+          # otherwise: the normal (uncapped or ignored) interpretation
+          input_clean <= breakpoints_current$breakpoint_S ~ as.sir("S"),
+          guideline_current %like% "EUCAST" & input_clean > breakpoints_current$breakpoint_R ~ as.sir("R"),
+          guideline_current %like% "CLSI" & input_clean >= breakpoints_current$breakpoint_R ~ as.sir("R"),
+
           # return "I" or "SDD" when breakpoints are in the middle
           !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == TRUE ~ as.sir("SDD"),
           !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
+
           # and NA otherwise
           TRUE ~ NA_sir_
         )
       } else if (method == "disk") {
         new_sir <- case_when_AMR(
-          is.na(values) ~ NA_sir_,
-          as.double(values) >= as.double(breakpoints_current$breakpoint_S) ~ as.sir("S"),
-          guideline_current %like% "EUCAST" & as.double(values) < as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
-          guideline_current %like% "CLSI" & as.double(values) <= as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
+          is.na(input_clean) ~ NA_sir_,
+          as.double(input_clean) >= as.double(breakpoints_current$breakpoint_S) ~ as.sir("S"),
+          guideline_current %like% "EUCAST" & as.double(input_clean) < as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
+          guideline_current %like% "CLSI" & as.double(input_clean) <= as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
           # return "I" or "SDD" when breakpoints are in the middle
           !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == TRUE ~ as.sir("SDD"),
           !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
@@ -1803,6 +1890,12 @@ as_sir_method <- function(method_short,
         )
       }
 
+      # rewrite S/R to WT/NWT if needed
+      if (isTRUE(as_wt_nwt)) {
+        new_sir[new_sir == "S"] <- "WT"
+        new_sir[new_sir == "R"] <- "NWT"
+      }
+
       # write to verbose output
       notes_current <- gsub("\n\n", "\n", trimws2(notes_current), fixed = TRUE)
       notes_current[notes_current == ""] <- NA_character_
@@ -1814,11 +1907,11 @@ as_sir_method <- function(method_short,
         ab_given = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
         mo_given = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
         host_given = vectorise_log_entry(host.bak[match(host_current, df$host)][1], length(rows)),
-        input_given = vectorise_log_entry(as.character(values_bak), length(rows)),
+        input_given = vectorise_log_entry(as.character(input_original), length(rows)),
         ab = vectorise_log_entry(breakpoints_current[, "ab", drop = TRUE], length(rows)),
         mo = vectorise_log_entry(breakpoints_current[, "mo", drop = TRUE], length(rows)),
         host = vectorise_log_entry(breakpoints_current[, "host", drop = TRUE], length(rows)),
-        input = vectorise_log_entry(as.character(values), length(rows)),
+        input = vectorise_log_entry(as.character(input_clean), length(rows)),
         outcome = vectorise_log_entry(as.sir(new_sir), length(rows)),
         notes = font_stripstyle(notes_current), # vectorise_log_entry(paste0(font_stripstyle(notes_current), collapse = "\n"), length(rows)),
         guideline = vectorise_log_entry(guideline_current, length(rows)),
@@ -1917,6 +2010,9 @@ pillar_shaft.sir <- function(x, ...) {
     out[x == "I"] <- font_orange_bg("  I  ")
     out[x == "R"] <- font_rose_bg("  R  ")
     out[x == "NI"] <- font_grey_bg(font_black("  NI "))
+    out[x == "WT"] <- font_green_bg(font_black("  WT "))
+    out[x == "NWT"] <- font_rose_bg(font_black(" NWT "))
+    out[x == "NS"] <- font_rose_bg(font_black("  NS "))
   }
   create_pillar_column(out, align = "left", width = 5)
 }
@@ -1974,33 +2070,18 @@ freq.sir <- function(x, ...) {
 # this prevents the requirement for putting the dependency in Imports:
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, sir)
 get_skimmers.sir <- function(column) {
-  # get the variable name 'skim_variable'
-  name_call <- function(.data) {
-    calls <- sys.calls()
-    frms <- sys.frames()
-    calls_txt <- vapply(calls, function(x) paste(deparse(x), collapse = ""), FUN.VALUE = character(1))
-    if (any(calls_txt %like% "skim_variable", na.rm = TRUE)) {
-      ind <- which(calls_txt %like% "skim_variable")[1L]
-      vars <- tryCatch(eval(parse(text = ".data$skim_variable$sir"), envir = frms[[ind]]),
-        error = function(e) NULL
-      )
-      tryCatch(ab_name(as.character(calls[[length(calls)]][[2]]), language = NULL, info = FALSE),
-        error = function(e) NA_character_
-      )
-    } else {
-      NA_character_
-    }
-  }
-
+  # TODO add here in AMR 3.1.0 details about guideline
   skimr::sfl(
     skim_type = "sir",
-    ab_name = name_call,
-    count_R = count_R,
-    count_S = count_susceptible,
+    # guideline = function(x) "EUCAST 2025", # or "Multiple"
+    # origin = function(x) "MIC", # or "Multiple"
+    count_S = count_S,
     count_I = count_I,
-    prop_R = ~ proportion_R(., minimum = 0),
-    prop_S = ~ susceptibility(., minimum = 0),
-    prop_I = ~ proportion_I(., minimum = 0)
+    count_R = count_R,
+    prop_S = ~ round(proportion_S(., minimum = 0) * 100, 1),
+    prop_I = ~ round(proportion_I(., minimum = 0) * 100, 1),
+    prop_R = ~ round(proportion_R(., minimum = 0) * 100, 1),
+    hist = ~ skimr::inline_hist(as.double(stats::na.omit(.)), 3)
   )
 }
 
@@ -2028,9 +2109,9 @@ print.sir <- function(x, ...) {
 #' @export
 as.double.sir <- function(x, ...) {
   dbls <- rep(NA_real_, length(x))
-  dbls[x == "S"] <- 1
-  dbls[x %in% c("SDD", "I")] <- 2
-  dbls[x == "R"] <- 3
+  dbls[x %in% c("S", "WT")] <- 1
+  dbls[x %in% c("I", "SDD")] <- 2
+  dbls[x %in% c("R", "NWT", "NS")] <- 3
   dbls
 }
 

R/sir_calc.R

@@ -41,7 +41,7 @@ sir_calc <- function(...,
                      as_percent = FALSE,
                      only_all_tested = FALSE,
                      only_count = FALSE) {
-  meet_criteria(ab_result, allow_class = c("character", "numeric", "integer"), has_length = c(1:5))
+  meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = seq_along(VALID_SIR_LEVELS), is_in = VALID_SIR_LEVELS)
   meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
   meet_criteria(as_percent, allow_class = "logical", has_length = 1)
   meet_criteria(only_all_tested, allow_class = "logical", has_length = 1)
@@ -117,6 +117,8 @@ sir_calc <- function(...,
   print_warning <- FALSE
 
   ab_result <- as.sir(ab_result)
+  denominator_vals <- levels(ab_result)
+  denominator_vals <- denominator_vals[denominator_vals != "NI"]
 
   if (is.data.frame(x)) {
     sir_integrity_check <- character(0)
@@ -148,7 +150,7 @@ sir_calc <- function(...,
       denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(anyNA(y))))
     } else {
       # may contain NAs in any column
-      other_values <- setdiff(c(NA, levels(ab_result)), ab_result)
+      other_values <- setdiff(c(NA, denominator_vals), ab_result)
       if ("SDD" %in% ab_result && "SDD" %in% unlist(x_transposed) && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
         message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
       }
@@ -165,7 +167,7 @@ sir_calc <- function(...,
       message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
     }
     numerator <- sum(x %in% ab_result, na.rm = TRUE)
-    denominator <- sum(x %in% levels(ab_result), na.rm = TRUE)
+    denominator <- sum(x %in% denominator_vals, na.rm = TRUE)
   }
 
   if (print_warning == TRUE) {
@@ -259,13 +261,13 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
   for (i in seq_len(ncol(data))) {
     # transform SIR columns
     if (is.sir(data[, i, drop = TRUE])) {
-      data[, i] <- as.character(data[, i, drop = TRUE])
+      data[, i] <- as.character(as.sir(data[, i, drop = TRUE]))
+      data[which(data[, i, drop = TRUE] %in% c("S", "SDD", "WT")), i] <- "S"
+      data[which(data[, i, drop = TRUE] %in% c("R", "NWT", "NS")), i] <- "R"
       if (isTRUE(combine_SI)) {
-        if ("SDD" %in% data[, i, drop = TRUE] && message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
-          message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
-        }
-        data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
+        data[which(data[, i, drop = TRUE] %in% c("I", "S")), i] <- "SI"
       }
+      data[which(!data[, i, drop = TRUE] %in% c("S", "SI", "I", "R")), i] <- NA_character_
     }
   }
 

R/tidymodels.R

@@ -1,20 +1,21 @@
 #' AMR Extensions for Tidymodels
 #'
-#' This family of functions allows using AMR-specific data types such as `<mic>` and `<sir>` inside `tidymodels` pipelines.
+#' This family of functions allows using AMR-specific data types such as `<sir>` and `<mic>` inside `tidymodels` pipelines.
 #' @inheritParams recipes::step_center
 #' @details
 #' You can read more in our online [AMR with tidymodels introduction](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
 #'
 #' Tidyselect helpers include:
-#' - [all_mic()] and [all_mic_predictors()] to select `<mic>` columns
-#' - [all_sir()] and [all_sir_predictors()] to select `<sir>` columns
+#' - [all_sir()] and [all_sir_predictors()] to select [`<sir>`][as.sir()] columns
+#' - [all_mic()] and [all_mic_predictors()] to select [`<mic>`][as.mic()] columns
+#' - [all_disk()] and [all_disk_predictors()] to select [`<disk>`][as.disk()] columns
 #'
 #' Pre-processing pipeline steps include:
-#' - [step_mic_log2()] to convert MIC columns to numeric (via `as.numeric()`) and apply a log2 transform, to be used with [all_mic_predictors()]
 #' - [step_sir_numeric()] to convert SIR columns to numeric (via `as.numeric()`), to be used with [all_sir_predictors()]: `"S"` = 1, `"I"`/`"SDD"` = 2, `"R"` = 3. All other values are rendered `NA`. Keep this in mind for further processing, especially if the model does not allow for `NA` values.
+#' - [step_mic_log2()] to convert MIC columns to numeric (via `as.numeric()`) and apply a log2 transform, to be used with [all_mic_predictors()]
 #'
 #' These steps integrate with `recipes::recipe()` and work like standard preprocessing steps. They are useful for preparing data for modelling, especially with classification models.
-#' @seealso [recipes::recipe()], [as.mic()], [as.sir()]
+#' @seealso [recipes::recipe()], [as.sir()], [as.mic()], [as.disk()]
 #' @name amr-tidymodels
 #' @keywords internal
 #' @export
@@ -66,35 +67,55 @@
 #'     bind_cols(out_testing)
 #'
 #'   # Evaluate predictions using standard classification metrics
-#'   our_metrics <- metric_set(accuracy, kap, ppv, npv)
+#'   our_metrics <- metric_set(accuracy,
+#'                             recall,
+#'                             precision,
+#'                             sensitivity,
+#'                             specificity,
+#'                             ppv,
+#'                             npv)
 #'   metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
 #'
 #'   # Show performance
 #'   metrics
 #' }
-all_mic <- function() {
-  x <- tidymodels_amr_select(levels(NA_mic_))
-  names(x)
-}
-
-#' @rdname amr-tidymodels
-#' @export
-all_mic_predictors <- function() {
-  x <- tidymodels_amr_select(levels(NA_mic_))
-  intersect(x, recipes::has_role("predictor"))
-}
-
-#' @rdname amr-tidymodels
-#' @export
 all_sir <- function() {
-  x <- tidymodels_amr_select(levels(NA_sir_))
+  x <- tidymodels_amr_select(class = "sir")
   names(x)
 }
 
 #' @rdname amr-tidymodels
 #' @export
 all_sir_predictors <- function() {
-  x <- tidymodels_amr_select(levels(NA_sir_))
+  x <- tidymodels_amr_select(class = "sir")
+  intersect(x, recipes::has_role("predictor"))
+}
+
+#' @rdname amr-tidymodels
+#' @export
+all_mic <- function() {
+  x <- tidymodels_amr_select(class = "mic")
+  names(x)
+}
+
+#' @rdname amr-tidymodels
+#' @export
+all_mic_predictors <- function() {
+  x <- tidymodels_amr_select(class = "mic")
+  intersect(x, recipes::has_role("predictor"))
+}
+
+#' @rdname amr-tidymodels
+#' @export
+all_disk <- function() {
+  x <- tidymodels_amr_select(class = "disk")
+  names(x)
+}
+
+#' @rdname amr-tidymodels
+#' @export
+all_disk_predictors <- function() {
+  x <- tidymodels_amr_select(class = "disk")
   intersect(x, recipes::has_role("predictor"))
 }
 
@@ -160,7 +181,6 @@ bake.step_mic_log2 <- function(object, new_data, ...) {
 print.step_mic_log2 <- function(x, width = max(20, options()$width - 35), ...) {
   title <- "Log2 transformation of MIC columns"
   recipes::print_step(x$columns, x$terms, x$trained, title, width)
-  invisible(x)
 }
 
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_mic_log2)
@@ -236,7 +256,6 @@ bake.step_sir_numeric <- function(object, new_data, ...) {
 print.step_sir_numeric <- function(x, width = max(20, options()$width - 35), ...) {
   title <- "Numeric transformation of SIR columns"
   recipes::print_step(x$columns, x$terms, x$trained, title, width)
-  invisible(x)
 }
 
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_sir_numeric)
@@ -250,13 +269,13 @@ tidy.step_sir_numeric <- function(x, ...) {
   res
 }
 
-tidymodels_amr_select <- function(check_vector) {
+tidymodels_amr_select <- function(class) {
   df <- get_current_data()
   ind <- which(
     vapply(
       FUN.VALUE = logical(1),
       df,
-      function(x) all(x %in% c(check_vector, NA), na.rm = TRUE) & any(x %in% check_vector),
+      function(x) inherits(x, class),
       USE.NAMES = TRUE
     ),
     useNames = TRUE

R/translate.R

@@ -263,19 +263,27 @@ translate_into_language <- function(from,
     df_trans$pattern[df_trans$regular_expr == TRUE] <- gsub("$$", "$", df_trans$pattern[df_trans$regular_expr == TRUE], fixed = TRUE)
   }
 
-  lapply(
-    # starting with longest pattern, since more general translations are shorter, such as 'Group'
-    order(nchar(df_trans$pattern), decreasing = TRUE),
-    function(i) {
-      from_unique_translated <<- gsub(
-        pattern = df_trans$pattern[i],
-        replacement = df_trans[i, lang, drop = TRUE],
-        x = from_unique_translated,
-        ignore.case = !df_trans$case_sensitive[i] & df_trans$regular_expr[i],
-        fixed = !df_trans$regular_expr[i],
-        perl = df_trans$regular_expr[i]
+  # non-regex part
+  translate_exec <- function(term) {
+    # sort trans file on length of pattern
+    trns <- df_trans[order(nchar(df_trans$pattern), decreasing = TRUE), ]
+    for (i in seq_len(nrow(trns))) {
+      term <- gsub(
+        pattern = trns$pattern[i],
+        replacement = trns[i, lang, drop = TRUE],
+        x = term,
+        ignore.case = !trns$case_sensitive[i] & trns$regular_expr[i],
+        fixed = !trns$regular_expr[i],
+        perl = trns$regular_expr[i],
       )
     }
+    term
+  }
+  from_unique_translated[order(nchar(from_unique_translated), decreasing = TRUE)] <- vapply(
+    FUN.VALUE = character(1),
+    USE.NAMES = FALSE,
+    from_unique_translated[order(nchar(from_unique_translated), decreasing = TRUE)],
+    translate_exec
   )
 
   # force UTF-8 for diacritics

R/zzz.R

@@ -115,6 +115,21 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
 }
 
 .onAttach <- function(libname, pkgname) {
+  if (interactive() && is.null(getOption("AMR_guideline"))) {
+    packageStartupMessage(
+      word_wrap(
+        "Welcome to AMR v", format(utils::packageVersion("AMR")), ". ",
+        "You have not set the 'AMR_guideline' option to either \"CLSI\" or \"EUCAST\". ",
+        "You can set it using either:\n",
+        "  options(AMR_guideline = \"CLSI\")\n",
+        "  options(AMR_guideline = \"EUCAST\")\n",
+        "See `?AMR-options`. While unset, the AMR package uses the current default guideline: ", AMR::clinical_breakpoints$guideline[1], ".",
+        add_fn = NULL
+      )
+    )
+  }
+
+
   # if custom ab option is available, load it
   if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
     if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {

README.Rmd

@@ -49,8 +49,11 @@ To install the latest 'beta' version:
 
 ```{r, eval = FALSE}
 install.packages("AMR", repos = "beta.amr-for-r.org")
+```
 
-# if this does not work, try to install directly from GitHub using the 'remotes' package:
+If this does not work, try to install directly from GitHub using the `remotes` package:
+
+```{r, eval = FALSE}
 remotes::install_github("msberends/AMR")
 ```
 

README.md

@@ -58,8 +58,12 @@ To install the latest ‘beta’ version:
 
 ``` r
 install.packages("AMR", repos = "beta.amr-for-r.org")
+```
 
-# if this does not work, try to install directly from GitHub using the 'remotes' package:
+If this does not work, try to install directly from GitHub using the
+`remotes` package:
+
+``` r
 remotes::install_github("msberends/AMR")
 ```
 

cran-comments.md

@@ -1,3 +1,5 @@
+This version is a bugfix release (v3.0.1) following the release of v3.0.0 in June 2025.
+
 As with all previous >20 releases, some CHECKs on `oldrel` may return a `NOTE` for narrowly exceeding the installation size limit. This has been reduced to a minimum in prior coordination with CRAN maintainers and currently returns only an `INFO` on `release` and `devel`.
 
 We treat this as a high-impact package: it was published in the *Journal of Statistical Software* (2022), is listed in the CRAN Task View "Epidemiology", and (based on cranlogs download statistics) is used globally. If there is anything to address, we would appreciate being informed before archiving the current version. We conduct extensive automated unit testing and have no indication of unresolved issues.

data-raw/_pre_commit_checks.R

@@ -368,7 +368,7 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
 pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
   filter(group %like% "aminoglycoside") %>%
   pull(ab)
-pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
+pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC"))
 pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>%
   filter(group %like% "antifungal") %>%
   pull(ab)
@@ -397,10 +397,6 @@ pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antimicrobials %>%
   filter(group %like% "cephalosporin.*5") %>%
   pull(ab)
 pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"]
-pre_commit_lst$AB_FLUOROQUINOLONES <- antimicrobials %>%
-  # see DOI 10.23937/2378-3656/1410369, more specifically this table: https://www.clinmedjournals.org/articles/cmrcr/cmrcr-8-369-table1.html
-  filter((group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone") & name %unlike% " acid|nalidixic|cinoxacin|flumequine|oxolinic|piromidic|pipemidic|rosoxacin") %>%
-  pull(ab)
 pre_commit_lst$AB_GLYCOPEPTIDES <- antimicrobials %>%
   filter(group %like% "glycopeptide") %>%
   pull(ab)
@@ -410,10 +406,10 @@ pre_commit_lst$AB_ISOXAZOLYLPENICILLINS <- antimicrobials %>%
 pre_commit_lst$AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
 pre_commit_lst$AB_GLYCOPEPTIDES_EXCEPT_LIPO <- pre_commit_lst$AB_GLYCOPEPTIDES[!pre_commit_lst$AB_GLYCOPEPTIDES %in% pre_commit_lst$AB_LIPOGLYCOPEPTIDES]
 pre_commit_lst$AB_LINCOSAMIDES <- antimicrobials %>%
-  filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2) & name %like% "^(pirlimycin)" & name %unlike% "screening|inducible")) %>%
+  filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2) & name %like% "^(pirlimycin|clinda)")) %>%
   pull(ab)
 pre_commit_lst$AB_MACROLIDES <- antimicrobials %>%
-  filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %like% "^(acetylmidecamycin|acetylspiramycin|gamith?romycin|kitasamycin|meleumycin|nafith?romycin|solith?romycin|tildipirosin|tilmicosin|tulath?romycin|tylosin|tylvalosin)" & name %unlike% "screening|inducible")) %>%
+  filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2)) | name %like% "^(acetylmidecamycin|acetylspiramycin|gamith?romycin|kitasamycin|meleumycin|nafith?romycin|primycin|solith?romycin|tildipirosin|tilmicosin|tulath?romycin|tylosin|tylvalosin)") %>%
   pull(ab)
 pre_commit_lst$AB_MONOBACTAMS <- antimicrobials %>%
   filter(group %like% "monobactam") %>%
@@ -430,36 +426,131 @@ pre_commit_lst$AB_PENICILLINS <- antimicrobials %>%
 pre_commit_lst$AB_PHENICOLS <- antimicrobials %>%
   filter(group %like% "phenicol" | atc_group1 %like% "phenicol" | atc_group2 %like% "phenicol") %>%
   pull(ab)
+pre_commit_lst$AB_PHOSPHONICS <- antimicrobials %>%
+  filter(group %like% "phosphonic" | name %like% "fosfo") %>%
+  pull(ab)
 pre_commit_lst$AB_POLYMYXINS <- antimicrobials %>%
   filter(group %like% "polymyxin") %>%
   pull(ab)
 pre_commit_lst$AB_QUINOLONES <- antimicrobials %>%
-  filter(group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone") %>%
+  filter(group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone" | name %like% "ozenoxacin") %>%
+  pull(ab)
+pre_commit_lst$AB_FLUOROQUINOLONES <- antimicrobials %>%
+  # see DOI 10.23937/2378-3656/1410369, more specifically this table: https://www.clinmedjournals.org/articles/cmrcr/cmrcr-8-369-table1.html
+  filter(ab %in% pre_commit_lst$AB_QUINOLONES & name %unlike% " acid|nalidixic|cinoxacin|flumequine|oxolinic|ozenoxacin|piromidic|pipemidic|rosoxacin") %>%
   pull(ab)
 pre_commit_lst$AB_RIFAMYCINS <- antimicrobials %>%
   filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
   pull(ab)
+pre_commit_lst$AB_SPIROPYRIMIDINETRIONES <- antimicrobials %>%
+  filter(name %like% "zoliflodacin") %>%
+  pull(ab)
 pre_commit_lst$AB_STREPTOGRAMINS <- antimicrobials %>%
   filter(atc_group2 %like% "streptogramin") %>%
   pull(ab)
 pre_commit_lst$AB_TETRACYCLINES <- antimicrobials %>%
-  filter(group %like% "tetracycline") %>%
+  filter(atc_group1 %like% "tetracycline" | atc_group2 %like% "tetracycline" | name %like% "chlortetracycline|cetocycline|demeclocycline|doxycycline|eravacycline|lymecycline|meclocycline|meth?acycline|minocycline|omadacycline|oxytetracycline|rolitetracycline|sarecycline|tetracycline|tigecycline") %>%
   pull(ab)
 pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"]
 pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>%
-  filter(group %like% "trimethoprim") %>%
+  filter(atc_group1 %like% "trimethoprim" | atc_group2 %like% "trimethoprim" | name %like% "trimethoprim|ormetroprim|iclaprim") %>%
   pull(ab)
 pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>%
-  filter(group %like% "trimethoprim" & name %unlike% "trimethoprim") %>%
+  filter(name %like% "(^|/)sulf[oai]") %>%
   pull(ab)
 pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
-pre_commit_lst$AB_BETALACTAMS <- sort(c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS, pre_commit_lst$AB_MONOBACTAMS))
+pre_commit_lst$AB_BETALACTAMS <- sort(c(
+  pre_commit_lst$AB_PENICILLINS,
+  pre_commit_lst$AB_CEPHALOSPORINS,
+  pre_commit_lst$AB_CARBAPENEMS,
+  pre_commit_lst$AB_MONOBACTAMS))
+pre_commit_lst$AB_BETALACTAMASE_INHIBITORS <- antimicrobials %>%
+  filter(atc_group2 %like% "Beta-lactamase inhibitors" | name %like% "bactam") %>%
+  pull(ab)
+# for EUCAST:
 pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%
-  filter(name %like% "/" & name %unlike% "EDTA" & ab %in% pre_commit_lst$AB_BETALACTAMS) %>%
+  filter(ab %in% pre_commit_lst$AB_BETALACTAMS & name %like% "/" & name %unlike% "EDTA") %>%
   pull(ab)
 # this will be used for documentation:
 pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
 
+# Update the antimicrobials$group column
+usethis::ui_info("Updating 'group' column in antimicrobials data set from AB_* vectors")
+prettify_group_name <- function(name) {
+  raw <- gsub("^AB_", "", name)
+  pretty <- tools::toTitleCase(gsub("_", " ", tolower(raw)))
+  pretty[pretty %like% " (except|with) "] <- ""
+  pretty <- gsub(" (1st|2nd|3rd|4th|5th|6th)", " (\\1 gen.)", pretty)
+  pretty <- gsub("([Bb])eta[-]?", "\\1eta-", pretty)
+  pretty <- gsub(" Inhibitor", " inhibitor", pretty)
+  pretty <- pretty[pretty != ""]
+  return(pretty)
+}
+group_map <- vector("list", length = nrow(antimicrobials))
+names(group_map) <- antimicrobials$ab
+for (group_name in pre_commit_lst$DEFINED_AB_GROUPS) {
+  ab_vector <- pre_commit_lst[[group_name]]
+  pretty_name <- prettify_group_name(group_name)
+  for (ab in ab_vector) {
+    ab_chr <- as.character(ab)
+    group_map[[ab_chr]] <- sort(unique(c(group_map[[ab_chr]], pretty_name)))
+  }
+}
+for (i in seq_along(group_map)) {
+  if (is.null(group_map[[i]])) {
+    group_map[[i]] <- "Other"
+    if (antimicrobials$group[i] %unlike% "other") {
+      usethis::ui_warn("AB had a group but not anymore: ", antimicrobials$name[i], " (", antimicrobials$ab[i], "), was ", toString(antimicrobials$group[i]))
+    }
+  }
+  group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))]
+}
+
+# create priority list for ab_group()
+pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins",
+                                      "Isoxazolylpenicillins",
+                                      "Ureidopenicillins",
+                                      "Oxazolidinones",
+                                      "Carbapenems",
+                                      "Cephalosporins (1st gen.)",
+                                      "Cephalosporins (2nd gen.)",
+                                      "Cephalosporins (3rd gen.)",
+                                      "Cephalosporins (4th gen.)",
+                                      "Cephalosporins (5th gen.)",
+                                      "Cephalosporins",
+                                      "Penicillins",
+                                      "Monobactams",
+                                      "Aminoglycosides",
+                                      "Lipoglycopeptides",
+                                      "Glycopeptides",
+                                      "Lincosamides",
+                                      "Streptogramins",
+                                      "Macrolides",
+                                      "Nitrofurans",
+                                      "Phenicols",
+                                      "Phosphonics",
+                                      "Polymyxins",
+                                      "Fluoroquinolones",
+                                      "Quinolones",
+                                      "Rifamycins",
+                                      "Spiropyrimidinetriones",
+                                      "Trimethoprims",
+                                      "Sulfonamides",
+                                      "Tetracyclines",
+                                      "Antifungals",
+                                      "Antimycobacterials",
+                                      "Beta-lactams",
+                                      "Beta-lactamase inhibitors",
+                                      "Other")
+if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) {
+  stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", "))
+}
+for (i in seq_along(group_map)) {
+  group_map[[i]] <- intersect(pre_commit_lst$ABX_PRIORITY_LIST, group_map[[i]])
+}
+antimicrobials$group <- unname(group_map)
+usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")
+
 pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(antimicrobials)
 pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(antivirals)
 
@@ -646,7 +737,33 @@ files_changed <- function(paths = "^(R|data)/") {
 # Update URLs -------------------------------------------------------------
 if (files_changed()) {
   usethis::ui_info("Checking URLs for redirects")
-  invisible(urlchecker::url_update("."))
+  # Step 1: Get sources from tools (excluding man/)
+  sources <- tools:::url_db_from_package_sources(".")
+  sources <- sources[!grepl("^man/", sources$Parent), ]
+  # Step 2: Get URLs from .R files in R/
+  r_files <- list.files("R", pattern = "\\.R$", full.names = TRUE)
+  # Function to extract URLs from a file
+  extract_urls_from_file <- function(file_path) {
+    lines <- readLines(file_path, warn = FALSE)
+    urls <- stringr::str_extract_all(lines, "https?://[^\\s)\"'>]+")
+    urls <- unlist(urls)
+    if (length(urls) == 0) {
+      return(NULL)
+    }
+    # Remove trailing punctuation (e.g., .,), etc.)
+    urls <- stringr::str_replace(urls, "[\\.,;)]+$", "")
+    data.frame(
+      URL = urls,
+      Parent = gsub("^\\./", "", file_path),
+      stringsAsFactors = FALSE
+    )
+  }
+  r_file_urls <- do.call(rbind, lapply(r_files, extract_urls_from_file))
+  # Step 3: Combine the two sources
+  total <- rbind(sources, r_file_urls)
+  # Step 4: Check URLs and update
+  results <- urlchecker::url_check(db = total)
+  invisible(urlchecker::url_update(results = results))
 }
 
 # Style pkg ---------------------------------------------------------------
@@ -679,5 +796,6 @@ if (files_changed("README.Rmd") ||
 }
 
 # Finished ----------------------------------------------------------------
+rm(antimicrobials)
 usethis::ui_done("All done")
 suppressMessages(reset_AMR_locale())

data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R

@@ -912,6 +912,24 @@ antimicrobials <- antimicrobials %>%
       oral_ddd = NA_real_
     ))
 
+# add Taniborbactam and Cefepime/taniborbactam
+antimicrobials <- antimicrobials |>
+  mutate(ab = as.character(ab)) |>
+  bind_rows(
+    antimicrobials |>
+      filter(ab == "FPE") |>
+      mutate(ab = as.character(ab)) |>
+      mutate(ab = "FTA",
+             name = "Cefepime/taniborbactam",
+             cid = NA_real_),
+    antimicrobials |>
+      filter(ab == "TBP") |>
+      mutate(ab = as.character(ab)) |>
+      mutate(ab = "TAN",
+             name = "Taniborbactam",
+             cid = 76902493,
+             abbreviations = list("VNRX-5133"))
+  )
 
 
 # update ATC codes from WHOCC website -------------------------------------

data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R

@@ -35,24 +35,26 @@ library(readr)
 library(tidyr)
 devtools::load_all()
 
-# Install the WHONET software on Windows (http://www.whonet.org/software.html),
-# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
-# (for ASIARS-Net update, also copy C:\WHONET\Codes to the data-raw/WHONET/ folder)
-
 # BE SURE TO RUN data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R FIRST TO GET THE GROUPS!
 
 # READ DATA ----
 
-whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) |>
+# files are retrieved from https://github.com/AClark-WHONET/AMRIE
+
+github_repo <- "https://raw.github.com/AClark-WHONET/AMRIE/main/Interpretation%20Engine/Resources"
+file_organisms <- file.path(github_repo, "Organisms.txt")
+file_breakpoints <- file.path(github_repo, "Breakpoints.txt")
+file_antibiotics <- file.path(github_repo, "Antibiotics.txt")
+
+whonet_organisms <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
   # remove old taxonomic names
   filter(TAXONOMIC_STATUS == "C") |>
   mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
 
-whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"),
-                               show_col_types = FALSE, guess_max = Inf) |>
+whonet_breakpoints <- read_tsv(file_breakpoints, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
   filter(GUIDELINES %in% c("CLSI", "EUCAST"))
 
-whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na = c("", "NA", "-"), show_col_types = FALSE) |>
+whonet_antibiotics <- read_tsv(file_antibiotics, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
   arrange(WHONET_ABX_CODE) |>
   distinct(WHONET_ABX_CODE, .keep_all = TRUE)
 

data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R

@@ -27,7 +27,7 @@
 # how to conduct AMR data analysis: https://amr-for-r.org              #
 # ==================================================================== #
 
-# This data set is being used in the clinical_breakpoints data set, and thus by as.sir().
+# This data set is being referenced from in the clinical_breakpoints data set, and also by as.sir().
 # It prevents the breakpoints table from being extremely long for species that are part of a species group.
 # Also used by eucast_rules() to expand group names.
 
@@ -36,10 +36,6 @@ library(readr)
 library(tidyr)
 devtools::load_all()
 
-# Install the WHONET software on Windows (http://www.whonet.org/software.html),
-# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
-
-
 # BACTERIAL COMPLEXES
 # find all bacterial complex in the NCBI Taxonomy Browser here:
 # https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=6&lin=f&keep=1&srchmode=1&unlock
@@ -48,9 +44,14 @@ devtools::load_all()
 
 # READ DATA ----
 
-whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
+# files are retrieved from https://github.com/AClark-WHONET/AMRIE
+
+github_repo <- "https://raw.github.com/AClark-WHONET/AMRIE/main/Interpretation%20Engine/Resources"
+file_organisms <- file.path(github_repo, "Organisms.txt")
+
+whonet_organisms <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
   # remove old taxonomic names
-  filter(TAXONOMIC_STATUS == "C") %>%
+  filter(TAXONOMIC_STATUS == "C") |>
   mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
 
 whonet_organisms <- whonet_organisms %>%
@@ -87,7 +88,7 @@ microorganisms.groups <- whonet_organisms %>%
             mo = ifelse(is.na(mo),
                         as.character(as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0)),
                         mo)) %>% 
-  # add our own CoNS and CoPS, WHONET does not strictly follow Becker et al (2014, 2019, 2020)
+  # add our own CoNS and CoPS, WHONET does not strictly follow Becker et al. (2014, 2019, 2020)
   filter(mo_group != as.mo("CoNS")) %>% 
   bind_rows(tibble(mo_group = as.mo("CoNS"), mo = MO_CONS)) %>% 
   filter(mo_group != as.mo("CoPS")) %>% 
@@ -153,7 +154,7 @@ microorganisms.groups <- whonet_organisms %>%
   filter(mo_group != "B_YERSN_PSDT-C") %>% 
   bind_rows(tibble(mo_group = as.mo("B_YERSN_PSDT-C"),
                    mo = paste("Yersinia", c("pseudotuberculosis", "pestis", "similis", "wautersii")) %>% as.mo(keep_synonyms = TRUE))) %>% 
-  # RGM are Rapidly-grwoing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
+  # RGM are Rapidly-growing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
   filter(mo_group != "B_MYCBC_RGM") %>% 
   bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),
                    mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE)))

data-raw/ab.md5

@@ -1 +1 @@
-228840b3941753c4adee2b781d901590
+17cd1c8d89d7fca96fe7e1e761a75dfa

data-raw/datasets/antimicrobials.txt

@@ -1,498 +1,499 @@
 "ab"	"cid"	"name"	"group"	"atc"	"atc_group1"	"atc_group2"	"abbreviations"	"synonyms"	"oral_ddd"	"oral_units"	"iv_ddd"	"iv_units"	"loinc"
 "AMA"	4649	"4-aminosalicylic acid"	"Antimycobacterials"	"J04AA01"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	"NA"	"aminacyl,aminopar,aminosalyl,aminox,apacil,deapasil,entepas,gabbropas,granupas,helipidyl,hellipidyl,nemasol,nippas,osacyl,pamacyl,pamisyl,paramisan,paramycin,parasal,parasalicil,parasalindon,pasade,pasalon,pasara,pascorbic,pasdium,pasem,paser,pasmed,pasnal,pasnodia,pasolac,passodico,pharmakon,propasa,rezipas,salvis,sanipirol,sanipriol,sodiopas,spectrum"	12	"g"			"NA"
-"ACM"	6450012	"Acetylmidecamycin"	"Macrolides/lincosamides"	"NA"			"NA"	"NA"					"NA"
-"ASP"	49787020	"Acetylspiramycin"	"Macrolides/lincosamides"	"NA"			"NA"	"antibiotic,espiramicin,espiramicina,foromacidin,provamycin,rovamicina,rovamycin,rovamycine,selectomycin,sequamycin,spiramycine,spiramycinum"					"NA"
-"ALS"	8954	"Aldesulfone sodium"	"Other antibacterials"	"J04BA03"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"NA"	"adesulfone,aldapsone,aldesulfone,aldesulphone,diamidin,diason,diasone,diasoneenterab,diazon,didimethanesulfinate,novotrone,sulfoxone"	0.33	"g"			"NA"
+"ACM"	6450012	"Acetylmidecamycin"	"Macrolides"	"NA"			"NA"	"NA"					"NA"
+"ASP"	49787020	"Acetylspiramycin"	"Macrolides"	"NA"			"NA"	"antibiotic,espiramicin,espiramicina,foromacidin,provamycin,rovamicina,rovamycin,rovamycine,selectomycin,sequamycin,spiramycine,spiramycinum"					"NA"
+"ALS"	8954	"Aldesulfone sodium"	"Other"	"J04BA03"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"NA"	"adesulfone,aldapsone,aldesulfone,aldesulphone,diamidin,diason,diasone,diasoneenterab,diazon,didimethanesulfinate,novotrone,sulfoxone"	0.33	"g"			"NA"
 "AMK"	37768	"Amikacin"	"Aminoglycosides"	"D06AX12,J01GB06,QD06AX12,QJ01GB06,QS01AA21,S01AA21"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"ak,ami,amik,amikac,amk,an"	"amikacillin,amikacina,amikacine,amikacinum,amikavet,amikin,amikozit,amukin,arikace,briclin,butirosins,kaminax,lukadin,mikavir,potentox,prestwick"			1	"g"	"101493-5,11-7,12-5,13-3,13546-7,14-1,15098-7,17798-0,18860-7,20373-7,23624-0,25174-4,25175-1,25176-9,25177-7,25178-5,25179-3,31097-9,31098-7,31099-5,3319-1,3320-9,3321-7,35669-1,42642-9,48169-7,50802-8,50803-6,56628-1,59378-0,60564-2,60565-9,6975-7,80972-3,89484-0"
-"AKF"		"Amikacin/fosfomycin"	"Aminoglycosides"	"NA"			"NA"	"NA"					"NA"
-"AMO"	54260	"Amorolfine"	"Antifungals/antimycotics"	"D01AE16,QD01AE16"	"Antifungals for topical use"	"Other antifungals for topical use"	"amor"	"amorolfina,amorolfinum,bekiron,corbel,curanail,fenpropemorph,fenpropimorph,fenpropimorphe,forbel,funbas,loceryl,locetar,mildofix,mistral,morpholine,odenil,omicur,pekiron"					"NA"
-"AMX"	33613	"Amoxicillin"	"Beta-lactams/penicillins"	"J01CA04,QG51AA03,QJ01CA04"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"ac,amox,amoxic,amx"	"acuotricina,alfamox,alfida,amitron,amoclen,amodex,amoksicillin,amolin,amopen,amopenixin,amophar,amoran,amoxi,amoxicaps,amoxicilina,amoxicilline,amoxicillinum,amoxidal,amoxiden,amoxil,amoxillat,amoxina,amoxine,amoxipen,amoxivet,amoxycillin,amoxycillinsalt,amoxyke,anemolin,aspenil,atoksilin,bristamox,cemoxin,ciblor,clamoxyl,damoxy,danoxillin,delacillin,demoksil,dispermox,efpenix,eupen,flemoxin,flemoxine,galenamox,gramidil,hiconcil,himinomax,histocillin,ibiamox,imacillin,izoltil,kentrocyllin,lamoxy,largopen,larotid,matasedrin,metifarma,moksilin,moxacin,moxal,moxaline,moxatag,neotetranase,novabritine,ospamox,pacetocin,pamocil,paradroxil,pasetocin,penamox,piramox,promoxil,quimiopen,remoxil,riotapen,robamox,sawacillin,siganopen,simplamox,sintopen,sumox,topramoxin,trifamox,trimox,unicillin,utimox,velamox,vetramox,wymox,zamocillin,zamocilline,zimox"	1.5	"g"	3	"g"	"101498-4,15-8,16-6,16365-9,17-4,18-2,18861-5,18862-3,19-0,20-8,21-6,22-4,25274-2,25310-4,3344-9,55614-2,55615-9,55616-7,6976-5,6977-3,80133-2"
-"AMC"	23665637	"Amoxicillin/clavulanic acid"	"Beta-lactams/penicillins"	"J01CR02,QJ01CR02"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/c,amcl,aml,amocla,aug,xl"	"amocla,amoclan,amoclav,amoksiclav,amoxsiklav,amoxyclav,ancla,augmentan,augmentin,augmentine,auspilic,clamentin,clamobit,clavam,clavamox,clavinex,clavumox,coamoxiclav,curam,eumetinex,kesium,kmoxilin,spectramox,synulox,viaclav,xiclav"	1.5	"g"	3	"g"	"NA"
-"AXS"	465441	"Amoxicillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR02,QJ01CR02"			"NA"	"NA"	1.5	"g"	3	"g"	"55614-2,55615-9,55616-7"
-"AMB"	5280965	"Amphotericin B"	"Antifungals/antimycotics"	"A01AB04,A07AA07,G01AA03,J02AA01,QA01AB04,QA07AA07,QG01AA03,QJ02AA01"	"Antimycotics for systemic use"	"Antibiotics"	"amf,amfb,amph,amphot"	"abelcet,abelecet,ambil,ambisome,amphocin,amphomoronal,amphotec,amphotericin,amphotocerin,amphozone,funganiline,fungilin,fungisome,fungisone,fungizone,halizon,nystatine,nystatinum,terrastatin"	40	"mg"	210	"mg"	"16370-9,18863-1,23-2,24-0,25-7,26-5,3353-0,3354-8,40707-2,40757-7,49859-2,6978-1"
-"AMH"		"Amphotericin B-high"	"Antifungals/antimycotics"	"NA"			"amfo b high,amhl,ampho b high,amphotericin high"	"NA"					"NA"
-"AMP"	6249	"Ampicillin"	"Beta-lactams/penicillins"	"J01CA01,QJ01CA01,QJ51CA01,QS01AA19,S01AA19"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"am,amp,amp100,amp200,ampi,ampici"	"adobacillin,alpen,amblosin,amcap,amcill,amfipen,ampen,amperil,ampichel,ampicilina,ampicillina,ampicilline,ampicillinesalt,ampicillinsalt,ampicillinum,ampifarm,ampikel,ampimed,ampinova,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,austrapen,bayer,binotal,bonapicillin,britacil,cimex,citteral,copharcilin,cymbi,delcillin,deripen,divercillin,doktacillin,domicillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,omnipen,orbicilina,penbristol,penbritin,penbrock,penialmen,penicline,penimic,penizillin,pensyn,pentrex,pentrexl,pentrexyl,pentritin,ponecil,princillin,principen,racenacillin,redicilin,rosampline,roscillin,semicillin,servicillin,sumipanto,supen,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trafarbiot,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,vidocillin,wypicil"	2	"g"	6	"g"	"101477-8,101478-6,18864-9,18865-6,20374-5,21066-6,23618-2,27-3,28-1,29-9,30-7,31-5,32-3,33-1,3355-5,33562-0,33919-2,34-9,43883-8,43884-6,6979-9,6980-7,87604-5"
-"SAM"	119561	"Ampicillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR01,QJ01CR01"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/s,ab,ampsul,ams,amsu,apsu,sam"	"sulacillin"			6	"g"	"101478-6,18865-6,20374-5,23618-2,31-5,32-3,33-1,34-9,6980-7"
-"AMR"	73341	"Amprolium"	"Other antibacterials"	"QP51BX02"			"NA"	"amprol,amprolio,amprovine,anticoccid,cocciprol,corid,mepyrium,picolinium,pyridinium,thiacoccid"					"NA"
-"ANI"	166548	"Anidulafungin"	"Antifungals/antimycotics"	"J02AX06,QJ02AX06"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"anid,anidul"	"anidulafungina,anidulafungine,anidulafunginum,biafungin,ecalta,eraxis"			0.1	"g"	"55343-8,57095-2,58420-1,77162-6"
-"APL"	6602341	"Apalcillin"	"Beta-lactams/penicillins"	"NA"			"apalci"	"apalcilina,apalcilline,apalcillinsalt,apalcillinum,lumota"					"NA"
+"AKF"		"Amikacin/fosfomycin"	"Aminoglycosides,Phosphonics"	"NA"			"NA"	"NA"					"NA"
+"AMO"	54260	"Amorolfine"	"Antifungals"	"D01AE16,QD01AE16"	"Antifungals for topical use"	"Other antifungals for topical use"	"amor"	"amorolfina,amorolfinum,bekiron,corbel,curanail,fenpropemorph,fenpropimorph,fenpropimorphe,forbel,funbas,loceryl,locetar,mildofix,mistral,morpholine,odenil,omicur,pekiron"					"NA"
+"AMX"	33613	"Amoxicillin"	"Aminopenicillins,Penicillins,Beta-lactams"	"J01CA04,QG51AA03,QJ01CA04"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"ac,amox,amoxic,amx"	"acuotricina,alfamox,alfida,amitron,amoclen,amodex,amoksicillin,amolin,amopen,amopenixin,amophar,amoran,amoxi,amoxicaps,amoxicilina,amoxicilline,amoxicillinum,amoxidal,amoxiden,amoxil,amoxillat,amoxina,amoxine,amoxipen,amoxivet,amoxycillin,amoxycillinsalt,amoxyke,anemolin,aspenil,atoksilin,bristamox,cemoxin,ciblor,clamoxyl,damoxy,danoxillin,delacillin,demoksil,dispermox,efpenix,eupen,flemoxin,flemoxine,galenamox,gramidil,hiconcil,himinomax,histocillin,ibiamox,imacillin,izoltil,kentrocyllin,lamoxy,largopen,larotid,matasedrin,metifarma,moksilin,moxacin,moxal,moxaline,moxatag,neotetranase,novabritine,ospamox,pacetocin,pamocil,paradroxil,pasetocin,penamox,piramox,promoxil,quimiopen,remoxil,riotapen,robamox,sawacillin,siganopen,simplamox,sintopen,sumox,topramoxin,trifamox,trimox,unicillin,utimox,velamox,vetramox,wymox,zamocillin,zamocilline,zimox"	1.5	"g"	3	"g"	"101498-4,15-8,16-6,16365-9,17-4,18-2,18861-5,18862-3,19-0,20-8,21-6,22-4,25274-2,25310-4,3344-9,55614-2,55615-9,55616-7,6976-5,6977-3,80133-2"
+"AMC"	23665637	"Amoxicillin/clavulanic acid"	"Aminopenicillins,Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"J01CR02,QJ01CR02"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/c,amcl,aml,amocla,aug,xl"	"amocla,amoclan,amoclav,amoksiclav,amoxsiklav,amoxyclav,ancla,augmentan,augmentin,augmentine,auspilic,clamentin,clamobit,clavam,clavamox,clavinex,clavumox,coamoxiclav,curam,eumetinex,kesium,kmoxilin,spectramox,synulox,viaclav,xiclav"	1.5	"g"	3	"g"	"NA"
+"AXS"	465441	"Amoxicillin/sulbactam"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"J01CR02,QJ01CR02"			"NA"	"NA"	1.5	"g"	3	"g"	"55614-2,55615-9,55616-7"
+"AMB"	5280965	"Amphotericin B"	"Antifungals"	"A01AB04,A07AA07,G01AA03,J02AA01,QA01AB04,QA07AA07,QG01AA03,QJ02AA01"	"Antimycotics for systemic use"	"Antibiotics"	"amf,amfb,amph,amphot"	"abelcet,abelecet,ambil,ambisome,amphocin,amphomoronal,amphotec,amphotericin,amphotocerin,amphozone,funganiline,fungilin,fungisome,fungisone,fungizone,halizon,nystatine,nystatinum,terrastatin"	40	"mg"	210	"mg"	"16370-9,18863-1,23-2,24-0,25-7,26-5,3353-0,3354-8,40707-2,40757-7,49859-2,6978-1"
+"AMH"		"Amphotericin B-high"	"Antifungals"	"NA"			"amfo b high,amhl,ampho b high,amphotericin high"	"NA"					"NA"
+"AMP"	6249	"Ampicillin"	"Aminopenicillins,Penicillins,Beta-lactams"	"J01CA01,QJ01CA01,QJ51CA01,QS01AA19,S01AA19"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"am,amp,amp100,amp200,ampi,ampici"	"adobacillin,alpen,amblosin,amcap,amcill,amfipen,ampen,amperil,ampichel,ampicilina,ampicillina,ampicilline,ampicillinesalt,ampicillinsalt,ampicillinum,ampifarm,ampikel,ampimed,ampinova,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,austrapen,bayer,binotal,bonapicillin,britacil,cimex,citteral,copharcilin,cymbi,delcillin,deripen,divercillin,doktacillin,domicillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,omnipen,orbicilina,penbristol,penbritin,penbrock,penialmen,penicline,penimic,penizillin,pensyn,pentrex,pentrexl,pentrexyl,pentritin,ponecil,princillin,principen,racenacillin,redicilin,rosampline,roscillin,semicillin,servicillin,sumipanto,supen,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trafarbiot,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,vidocillin,wypicil"	2	"g"	6	"g"	"101477-8,101478-6,18864-9,18865-6,20374-5,21066-6,23618-2,27-3,28-1,29-9,30-7,31-5,32-3,33-1,3355-5,33562-0,33919-2,34-9,43883-8,43884-6,6979-9,6980-7,87604-5"
+"SAM"	119561	"Ampicillin/sulbactam"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"J01CR01,QJ01CR01"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/s,ab,ampsul,ams,amsu,apsu,sam"	"sulacillin"			6	"g"	"101478-6,18865-6,20374-5,23618-2,31-5,32-3,33-1,34-9,6980-7"
+"AMR"	73341	"Amprolium"	"Other"	"QP51BX02"			"NA"	"amprol,amprolio,amprovine,anticoccid,cocciprol,corid,mepyrium,picolinium,pyridinium,thiacoccid"					"NA"
+"ANI"	166548	"Anidulafungin"	"Antifungals"	"J02AX06,QJ02AX06"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"anid,anidul"	"anidulafungina,anidulafungine,anidulafunginum,biafungin,ecalta,eraxis"			0.1	"g"	"55343-8,57095-2,58420-1,77162-6"
+"APL"	6602341	"Apalcillin"	"Penicillins,Beta-lactams"	"NA"			"apalci"	"apalcilina,apalcilline,apalcillinsalt,apalcillinum,lumota"					"NA"
 "APR"	3081545	"Apramycin"	"Aminoglycosides"	"QA07AA92,QJ01GB90,QJ51GB90"			"apramy"	"ambylan,apralan,apramicina,apramycine,apramycinum"					"23659-6,73652-0,73653-8"
 "ARB"	68682	"Arbekacin"	"Aminoglycosides"	"J01GB12,QJ01GB12"			"arbeka"	"arbekacina,arbekacine,arbekacinum,haberacin"			0.2	"g"	"32373-3,53818-1,54173-0"
-"APX"	71961	"Aspoxicillin"	"Beta-lactams/penicillins"	"J01CA19,QJ01CA19"			"apoxic,aspoxi"	"aspoxicilina,aspoxicillan,aspoxicilline,aspoxicillinum,doyle"			4	"g"	"NA"
+"APX"	71961	"Aspoxicillin"	"Penicillins,Beta-lactams"	"J01CA19,QJ01CA19"			"apoxic,aspoxi"	"aspoxicilina,aspoxicillan,aspoxicilline,aspoxicillinum,doyle"			4	"g"	"NA"
 "AST"	5284517	"Astromicin"	"Aminoglycosides"	"NA"			"astrom"	"abbott,astromicina,astromicine,astromicinum,fortimicin,istamycin,istamycins"					"NA"
-"AVB"	9835049	"Avibactam"	"Beta-lactams/penicillins"	"NA"			"NA"	"avibactamfreeacid"					"NA"
-"AVI"	71674	"Avilamycin"	"Other antibacterials"	"QA07AA95"			"avilam"	"avilamycina,avilamycine,avilamycinum,inteprity,kavault,surmax"					"35754-1,35755-8,35756-6,55619-1"
+"AVB"	9835049	"Avibactam"	"Beta-lactamase inhibitors"	"NA"			"NA"	"avibactamfreeacid"					"NA"
+"AVI"	71674	"Avilamycin"	"Other"	"QA07AA95"			"avilam"	"avilamycina,avilamycine,avilamycinum,inteprity,kavault,surmax"					"35754-1,35755-8,35756-6,55619-1"
 "AVO"	16131159	"Avoparcin"	"Glycopeptides"	"NA"			"NA"	"firvanq,tagocid,targocid,targosid,tecoplanina,tecoplanine,tecoplaninum,teichomycin,teicoplanina,teicoplanine,teicoplaninum,teikoplanin,ticocin"					"NA"
-"AZD"	15574941	"Azidocillin"	"Beta-lactams/penicillins"	"J01CE04,QJ01CE04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"azidocilina,azidocillina,azidocilline,azidocillinum"	1.5	"g"			"NA"
-"AZM"	447043	"Azithromycin"	"Macrolides/lincosamides"	"J01FA10,QJ01FA10,QS01AA26,S01AA26"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"az,azi,azit,azithr,azm"	"aritromicina,aruzilina,azasite,azenil,azifast,azigram,azimakrol,azithramycine,azithrocin,azithromycine,azithromycinum,azitrocin,azitromax,azitromicina,azitromicine,azitromin,aziwin,aziwok,aztrin,azyter,hemomycin,macrozit,misultina,mixoterin,setron,sumamed,tobil,toraseptol,tromix,trozocina,trulimax,xithrone,zentavion,zifin,zithrax,zithromac,zithromax,zitrim,zitromax,zitrotek,zythromax"	0.3	"g"	0.5	"g"	"100043-9,16420-2,16421-0,18866-4,23612-5,25233-8,35-6,36-4,37-2,38-0,6981-5,89480-8"
-"AFC"		"Azithromycin/fluconazole/secnidazole"	"Other antibacterials"	"J01RA07,QJ01RA07"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"AZL"	6479523	"Azlocillin"	"Beta-lactams/penicillins"	"J01CA09,QJ01CA09"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"az,azl,azlo,azloci"	"azlin,azlocilina,azlocilline,azlocillinsalt,azlocillinum,securopen"			12	"g"	"16422-8,18867-2,3368-8,39-8,40-6,41-4,41661-0,42-2"
-"ATM"	5742832	"Aztreonam"	"Monobactams"	"J01DF01,QJ01DF01"	"Other beta-lactam antibacterials"	"Monobactams"	"at,atm,azm,azt,azt1,aztr,aztreo"	"azactam,azetreonam,azonam,azthreonam,aztreon,aztreonamum,cayston,dynabiotic,nebactam,primbactam,squibb"			4	"g"	"101497-6,16423-6,18868-0,25234-6,3369-6,41662-8,41663-6,41664-4,41727-9,43-0,44-8,45-5,46-3,6982-3"
-"AZA"		"Aztreonam/avibactam"	"Monobactams"	"J01DF51,QJ01DF51"			"NA"	"NA"					"NA"
-"ANC"		"Aztreonam/nacubactam"	"Monobactams"	"J01DF51,QJ01DF51"			"NA"	"NA"					"NA"
-"BAM"	441397	"Bacampicillin"	"Beta-lactams/penicillins"	"J01CA06,QJ01CA06"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"bacamp"	"alphacilina,alphacillin,ambacamp,ambaxin,bacacil,bacampicilina,bacampicilline,bacampicillinum,bacampicine,berocillin,centurina,devonium,diancina,inacilin,maxifen,penglobe,pivatil,pondocil,pondocillin,pondocillina,sanguicillin,spectrobid,velbacil"	1.2	"g"			"18869-8,47-1,48-9,49-7,50-5,55620-9"
-"BAC"	78358334	"Bacitracin"	"Other antibacterials"	"D06AX05,J01XX10,QA07AA93,QD06AX05,QJ01XX10,QR02AB04,QS01AA32,R02AB04,S01AA32"			"baci,bacitr"	"albac,altracin,ayfivin,baciferm,baciguent,baciim,baciliquin,bacilliquin,baciquent,bacitracina,bacitracine,bacitracinum,fortracin,mycitracin,parentracin,penitracin,septa,topitracin,topitrasin,tropitracin,zutracin"					"10868-8,16428-5,18870-6,6827-0,6983-1,87603-7"
-"BDQ"	5388906	"Bedaquiline"	"Other antibacterials"	"J04AK05,QJ04AK05"			"NA"	"NA"	86	"mg"			"80637-2,88703-4,88704-2,94274-8,96107-8"
+"AZD"	15574941	"Azidocillin"	"Penicillins,Beta-lactams"	"J01CE04,QJ01CE04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"azidocilina,azidocillina,azidocilline,azidocillinum"	1.5	"g"			"NA"
+"AZM"	447043	"Azithromycin"	"Macrolides"	"J01FA10,QJ01FA10,QS01AA26,S01AA26"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"az,azi,azit,azithr,azm"	"aritromicina,aruzilina,azasite,azenil,azifast,azigram,azimakrol,azithramycine,azithrocin,azithromycine,azithromycinum,azitrocin,azitromax,azitromicina,azitromicine,azitromin,aziwin,aziwok,aztrin,azyter,hemomycin,macrozit,misultina,mixoterin,setron,sumamed,tobil,toraseptol,tromix,trozocina,trulimax,xithrone,zentavion,zifin,zithrax,zithromac,zithromax,zitrim,zitromax,zitrotek,zythromax"	0.3	"g"	0.5	"g"	"100043-9,16420-2,16421-0,18866-4,23612-5,25233-8,35-6,36-4,37-2,38-0,6981-5,89480-8"
+"AFC"		"Azithromycin/fluconazole/secnidazole"	"Other"	"J01RA07,QJ01RA07"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"AZL"	6479523	"Azlocillin"	"Ureidopenicillins,Penicillins,Beta-lactams"	"J01CA09,QJ01CA09"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"az,azl,azlo,azloci"	"azlin,azlocilina,azlocilline,azlocillinsalt,azlocillinum,securopen"			12	"g"	"16422-8,18867-2,3368-8,39-8,40-6,41-4,41661-0,42-2"
+"ATM"	5742832	"Aztreonam"	"Monobactams,Beta-lactams"	"J01DF01,QJ01DF01"	"Other beta-lactam antibacterials"	"Monobactams"	"at,atm,azm,azt,azt1,aztr,aztreo"	"azactam,azetreonam,azonam,azthreonam,aztreon,aztreonamum,cayston,dynabiotic,nebactam,primbactam,squibb"			4	"g"	"101497-6,16423-6,18868-0,25234-6,3369-6,41662-8,41663-6,41664-4,41727-9,43-0,44-8,45-5,46-3,6982-3"
+"AZA"		"Aztreonam/avibactam"	"Monobactams,Beta-lactams,Beta-lactamase inhibitors"	"J01DF51,QJ01DF51"			"NA"	"NA"					"NA"
+"ANC"		"Aztreonam/nacubactam"	"Monobactams,Beta-lactams,Beta-lactamase inhibitors"	"J01DF51,QJ01DF51"			"NA"	"NA"					"NA"
+"BAM"	441397	"Bacampicillin"	"Penicillins,Beta-lactams"	"J01CA06,QJ01CA06"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"bacamp"	"alphacilina,alphacillin,ambacamp,ambaxin,bacacil,bacampicilina,bacampicilline,bacampicillinum,bacampicine,berocillin,centurina,devonium,diancina,inacilin,maxifen,penglobe,pivatil,pondocil,pondocillin,pondocillina,sanguicillin,spectrobid,velbacil"	1.2	"g"			"18869-8,47-1,48-9,49-7,50-5,55620-9"
+"BAC"	78358334	"Bacitracin"	"Other"	"D06AX05,J01XX10,QA07AA93,QD06AX05,QJ01XX10,QR02AB04,QS01AA32,R02AB04,S01AA32"			"baci,bacitr"	"albac,altracin,ayfivin,baciferm,baciguent,baciim,baciliquin,bacilliquin,baciquent,bacitracina,bacitracine,bacitracinum,fortracin,mycitracin,parentracin,penitracin,septa,topitracin,topitrasin,tropitracin,zutracin"					"10868-8,16428-5,18870-6,6827-0,6983-1,87603-7"
+"BDQ"	5388906	"Bedaquiline"	"Other"	"J04AK05,QJ04AK05"			"NA"	"NA"	86	"mg"			"80637-2,88703-4,88704-2,94274-8,96107-8"
 "BEK"	439318	"Bekanamycin"	"Aminoglycosides"	"J01GB13,QJ01GB13"			"NA"	"aminodeoxykanamycin,becanamicina,bekanamicina,bekanamycine,bekanamycinum"			0.6	"g"	"NA"
-"BNB"		"Benzathine benzylpenicillin"	"Beta-lactams/penicillins"	"J01CE08,QJ01CE08"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"NA"			3.6	"g"	"NA"
-"BNP"	64725	"Benzathine phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"J01CE10,QJ01CE10"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"bicillin,biphecillin"	2	"g"			"NA"
-"PEN"	5904	"Benzylpenicillin"	"Beta-lactams/penicillins"	"J01CE01,QJ01CE01,QJ51CE01,QS01AA14,S01AA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	"bepe,pen,peni,peni g,penic8,penica,penici,penicillin,penicillin g,penora,pg"	"bencilpenicilina,benzopenicillin,benzylpenicilline,benzylpenicillinum,capicillin,cillora,cilloral,cilopen,cintrisul,cosmopen,cristapen,crystapen,dropcillin,eskacillin,falapen,forpen,galofak,gelacillin,hipercilina,hyasorb,hylenta,lemopen,liquacillin,liquapen,monocillin,monopen,mycofarm,novocillin,penalev,penicillinum,penilaryn,penisem,pentid,pentids,pfizerpen,pharmacillin,pradupen,scotcil,sugracillin,sugracillinsalt,tabilin,ursopen,veticillin"			3.6	"g"	"NA"
-"PEN-S"		"Benzylpenicillin screening test"	"Beta-lactams/penicillins"	"NA"			"pen screen"	"NA"					"NA"
-"BES"	10178705	"Besifloxacin"	"Fluoroquinolones"	"QS01AE08,S01AE08"			"besifl"	"besivance"					"73606-6,73628-0,73651-2"
+"BNB"		"Benzathine benzylpenicillin"	"Penicillins,Beta-lactams"	"J01CE08,QJ01CE08"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"NA"			3.6	"g"	"NA"
+"BNP"	64725	"Benzathine phenoxymethylpenicillin"	"Penicillins,Beta-lactams"	"J01CE10,QJ01CE10"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"bicillin,biphecillin"	2	"g"			"NA"
+"PEN"	5904	"Benzylpenicillin"	"Penicillins,Beta-lactams"	"J01CE01,QJ01CE01,QJ51CE01,QS01AA14,S01AA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	"bepe,pen,peni,peni g,penic8,penica,penici,penicillin,penicillin g,penora,pg"	"bencilpenicilina,benzopenicillin,benzylpenicilline,benzylpenicillinum,capicillin,cillora,cilloral,cilopen,cintrisul,cosmopen,cristapen,crystapen,dropcillin,eskacillin,falapen,forpen,galofak,gelacillin,hipercilina,hyasorb,hylenta,lemopen,liquacillin,liquapen,monocillin,monopen,mycofarm,novocillin,penalev,penicillinum,penilaryn,penisem,pentid,pentids,pfizerpen,pharmacillin,pradupen,scotcil,sugracillin,sugracillinsalt,tabilin,ursopen,veticillin"			3.6	"g"	"NA"
+"PEN-S"		"Benzylpenicillin screening test"	"Penicillins,Beta-lactams"	"NA"			"pen screen"	"NA"					"NA"
+"BES"	10178705	"Besifloxacin"	"Fluoroquinolones,Quinolones"	"QS01AE08,S01AE08"			"besifl"	"besivance"					"73606-6,73628-0,73651-2"
 "BLA-S"		"Beta-lactamase screening test"	"Other"	"NA"			"beta-lactamase,betalactamase,bl screen,blt screen"	"NA"					"NA"
-"BIA"	71339	"Biapenem"	"Carbapenems"	"J01DH05,QJ01DH05"			"biapen"	"biapenern,omegacin"			1.2	"g"	"41665-1,41666-9,41667-7,41728-7"
-"BCZ"	65807	"Bicyclomycin"	"Other antibacterials"	"NA"			"bicozamycin"	"aizumycin,bacfeed,bacteron,bicozamicina,bicozamycin,bicozamycine,bicozamycinum"					"NA"
+"BIA"	71339	"Biapenem"	"Carbapenems,Beta-lactams"	"J01DH05,QJ01DH05"			"biapen"	"biapenern,omegacin"			1.2	"g"	"41665-1,41666-9,41667-7,41728-7"
+"BCZ"	65807	"Bicyclomycin"	"Other"	"NA"			"bicozamycin"	"aizumycin,bacfeed,bacteron,bicozamicina,bicozamycin,bicozamycine,bicozamycinum"					"NA"
 "BLM"	5360373	"Bleomycin"	"Glycopeptides"	"L01DC01,QL01DC01"			"NA"	"blenamax,blenoxane,bleocin,bleomicin,bleomicina,bleomycine,bleomycins,bleomycinum,blexane,nbleomycinamide"					"NA"
 "BDP"	68760	"Brodimoprim"	"Trimethoprims"	"J01EA02,QJ01EA02"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	"NA"	"brodimoprima,brodimoprime,brodimoprimum,bromdimoprim,hyprim,unitrim"	0.2	"g"			"NA"
-"BUT"	47472	"Butoconazole"	"Antifungals/antimycotics"	"G01AF15,QG01AF15"			"NA"	"butaconazole,butoconazol,butoconazolum,gynofort"					"NA"
+"BUT"	47472	"Butoconazole"	"Antifungals"	"G01AF15,QG01AF15"			"NA"	"butaconazole,butoconazol,butoconazolum,gynofort"					"NA"
 "CDZ"	44242317	"Cadazolid"	"Oxazolidinones"	"NA"			"NA"	"NA"					"NA"
 "CLA"		"Calcium aminosalicylate"	"Antimycobacterials"	"J04AA03,QJ04AA03"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	"NA"	"NA"	15	"g"			"NA"
 "CAP"	135565060	"Capreomycin"	"Antimycobacterials"	"J04AB30,QJ04AB30"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"capr,capreo"	"NA"			1	"g"	"16545-6,18872-2,23607-5,25210-6,25211-4,25212-2,42643-7,48170-5,55-4,55623-3,56-2,57-0,58-8,61355-4,89483-2"
-"CRB"	20824	"Carbenicillin"	"Beta-lactams/penicillins"	"J01CA03,QJ01CA03"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"bar,carb,carben,cb"	"anabactyl,carbecin,carbenicilina,carbenicillina,carbenicilline,carbenicillinum,dicarbenicillin,dipenicillin,fugacillin,geopen,gripenin,hyoper,microcillin,piopen,pyocianil,pyoclox,pyopan,pyopen,pyopene"			12	"g"	"18873-0,3434-8,41668-5,59-6,60-4,61-2,62-0"
-"CRN"	93184	"Carindacillin"	"Beta-lactams/penicillins"	"J01CA05,QJ01CA05"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"carindacilina,carindacilline,carindacillinsalt,carindacillinum,geocillin,indanylcarbinicillin,urobac"	4	"g"			"NA"
-"CAR"	6540466	"Carumonam"	"Monobactams"	"J01DF02,QJ01DF02"			"NA"	"carumonamum"			2	"g"	"51694-8"
-"CAS"	2826718	"Caspofungin"	"Antifungals/antimycotics"	"J02AX04,QJ02AX04"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"casp,caspof"	"cancidas,caspofungina"			50	"mg"	"32378-2,54175-5,54176-3,54185-4,58419-3"
-"CAC"	91562	"Cefacetrile"	"Cephalosporins (1st gen.)"	"J01DB10,QJ01DB10,QJ51DB10"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cephac"	"cefacetril,cefacetrilo,cefacetrilum,celospor,cephacetrile,vetrimast"					"55624-1,55625-8,55626-6,55627-4"
-"CEC"	51039	"Cefaclor"	"Cephalosporins (2nd gen.)"	"J01DC04,QJ01DC04"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"ccl,cec,cefacl,cf,cfac,cfc,cfcl,cfr,fac"	"alenfral,alfacet,alfatil,ceclor,cefachlor,cefaclorum,cefeaclor,cephaclor,compound,distaclor,keflor,kefolor,kefral,keftab,keftid,lilly,lopac,panacef,panoral,raniclor"	1	"g"			"16564-7,18874-8,21149-0,6986-4,83-6,84-4,85-1,86-9"
-"CFR"	47965	"Cefadroxil"	"Cephalosporins (1st gen.)"	"J01DB05,QJ01DB05"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefadr,cfdx,cfr,fad"	"bidocel,cefadrops,cefadroxilo,cefadroxilum,cefradroxil,cefzil,cephadroxil,duracef,duricef,kefroxil,sumacef,ultracef"	2	"g"			"16565-4,18875-5,55628-2,63-8,64-6,65-3,66-1"
-"LEX"	27447	"Cefalexin"	"Cephalosporins (1st gen.)"	"J01DB01,QJ01DB01,QJ51DB01"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cepale,cflx"	"adcadina,alcephin,alsporin,ambal,amplex,aristosporin,azabort,bactopenor,beliam,biocef,carnosporin,cefablan,cefacet,cefadal,cefadin,cefadina,cefalekey,cefaleksin,cefalessina,cefalexgobens,cefalexina,cefalexine,cefalexinum,cefalin,cefalival,cefaloto,cefanex,cefaseptin,cefax,ceffanex,cefibacter,ceflax,ceforal,cefovit,celexin,cepastar,cepexin,cephacillin,cephalexine,cephalexinum,cephalobene,cephanasten,cephaxin,cephin,cepol,ceporex,ceporexin,ceporexine,cerexin,cerexins,check,cophalexin,domucef,doriman,durantel,efemida,erocetin,factagard,felexin,fexin,ibilex,ibrexin,inphalex,karilexina,kefalospes,keflet,keflex,kefolan,keforal,kekrinal,kidolex,lafarine,larixin,lenocef,lexibiotico,loisine,lonflex,lopilexin,losporal,madlexin,maksipor,mamalexin,mamlexin,medolexin,medoxine,neokef,neolexina,noveol,novolexin,nufex,optocef,oracef,oriphex,oroxin,ortisporina,ospexin,palitrex,panixine,pectril,prindex,pyassan,rilexine,roceph,rogevil,sanaxin,sartosona,sencephalin,sepexin,servicef,servispor,sialexin,sinthecillin,sintolexyn,sporicef,sporidex,syncl,syncle,synecl,taicelexin,tepaxin,theratrex,tokiolexin,uphalexin,viosporine,voxxim,winlex,zabytrex,zozarine"	2	"g"			"NA"
-"RID"	5773	"Cefaloridine"	"Cephalosporins (1st gen.)"	"J01DB02,QJ01DB02"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefa,ceplor"	"aliporina,ampligram,cefaloridin,cefaloridina,cefaloridinum,cefalorizin,ceflorin,cepaloridin,cepalorin,cephalomycine,cephaloridin,cephaloridine,cephaloridinum,ceporan,ceporin,ceporine,cilifor,deflorin,faredina,floridin,glaxoridin,intrasporin,keflodin,keflordin,kefloridin,kefspor,lloncefal,sasperin,sefacin,verolgin,vioviantine"			3	"g"	"NA"
-"CEP"	6024	"Cefalotin"	"Cephalosporins (1st gen.)"	"J01DB03,QJ01DB03"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cephal,cfal,cflt"	"averon,cefalothin,cefalothine,cefalothinsalt,cefalotina,cefalotine,cefalotinsalt,cefalotinum,cemastin,cephalothin,cephalothinsalt,cephalothinum,cephalotin,cephalotinsalt,ceporacin,cepovenin,coaxin,keflin,lospoven,microtin,seffin,synclotin,toricelocin"			4	"g"	"NA"
-"MAN"	456255	"Cefamandole"	"Cephalosporins (2nd gen.)"	"J01DC03,QJ01DC03"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefama,cfam,cfmn"	"cefadole,cefamandol,cefamandolum,cephadole,kefamandol,kefdole,mancef"			6	"g"	"18876-3,3441-3,41669-3,55634-0,55635-7,55636-5,55637-3,67-9,68-7,69-5,70-3"
-"HAP"	30699	"Cefapirin"	"Cephalosporins (1st gen.)"	"J01DB08,QG51AA05,QJ01DB08,QJ51DB08"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cephap"	"ambrocef,brisfirina,brisporin,bristocef,cefadyl,cefalak,cefaloject,cefapirina,cefapirine,cefapirinsalt,cefapirinum,cefaprin,cefatrex,cefatrexyl,cephapirin,cephapirine,cephapirinsalt,cephatrexil,cephatrexyl,metricure"			4	"g"	"NA"
-"CTZ"	6410758	"Cefatrizine"	"Cephalosporins (1st gen.)"	"J01DB07,QJ01DB07"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefatr"	"bricef,cefathiamidine,cefatrix,cefatrizino,cefatrizinum,cephatriazine,cepticol,cetrazil,latocef,orosporina,orotric,seapuron,trizina"	1	"g"			"18877-1,55639-9,71-1,72-9,73-7,74-5"
-"CZD"	71736	"Cefazedone"	"Cephalosporins (1st gen.)"	"J01DB06,QJ01DB06"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefaze"	"cefazedon,cefazedona,cefazedonesalt,cefazedonum,refosporen,refosporene,refosporin,refosporinsalt"			3	"g"	"NA"
-"CZO"	33255	"Cefazolin"	"Cephalosporins (1st gen.)"	"J01DB04,QJ01DB04,QJ51DB04"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefazo,cfz,cfzl,cz,czol,faz,kz"	"ancef,atirin,biazolina,cefabiozim,cefacidal,cefalomicina,cefamedin,cefamezin,cefazil,cefazina,cefazolina,cefazoline,cefazolinsalt,cefazolinum,cephamezine,cephazolidin,cephazolin,cephazoline,elzogram,firmacef,gramaxin,kefzol,lampocef,liviclina,neofazol,oprea,recef,totacef,zolicef,zolisint"			3	"g"	"16566-2,18878-9,25235-3,3442-1,3443-9,41670-1,75-2,76-0,77-8,78-6,80962-4,85422-4"
-"CFB"	127527	"Cefbuperazone"	"Other antibacterials"	"J01DC13,QJ01DC13"			"cefbup"	"cefbuperazona,cefbuperazonesalt,cefbuperazonum,cefbuperzaone,cerbuperazone,keiperazon,tomiporan"			2	"g"	"NA"
-"CCP"	6436055	"Cefcapene"	"Cephalosporins (3rd gen.)"	"J01DD17,QJ01DD17"			"cefcap"	"flomox"	0.45	"g"			"100044-7,76143-7"
-"CCX"	5282438	"Cefcapene pivoxil"	"Cephalosporins (3rd gen.)"	"NA"			"NA"	"cefcamate,flumax"					"NA"
-"CDR"	6915944	"Cefdinir"	"Cephalosporins (3rd gen.)"	"J01DD15,QJ01DD15"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cd,cdn,cdr,cefdin,cfd,din"	"cefdinirum,cefdinyl,cefdirnir,ceftinex,cefzon,omnicef"	0.6	"g"			"23636-4,23637-2,35757-4,35758-2"
-"DIT"	9870843	"Cefditoren"	"Cephalosporins (3rd gen.)"	"J01DD16,QJ01DD16"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cdn,cefdit"	"cefditoreno,spectracef"	0.4	"g"			"35759-0,35760-8,35761-6,35762-4"
-"DIX"	6437877	"Cefditoren pivoxil"	"Cephalosporins (3rd gen.)"	"NA"			"NA"	"cefditorin,meiact,pivaloyloxymethyl"					"NA"
-"FEP"	5479537	"Cefepime"	"Cephalosporins (4th gen.)"	"J01DE01,QJ01DE01"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"cefep4,cefepi,cfep,cfpi,cpe,cpm,fep,pm,xpm"	"anticefepime,axepim,cefepima,cefepimum,maxipime,pyrrolidinium,renapime"			4	"g"	"101502-3,18879-7,31142-3,31143-1,35763-2,38363-8,42350-9,42351-7,42353-3,50631-1,58412-8,6643-1,6644-9,6645-7,6646-5,6987-2,8272-7,8273-5"
-"CFA"		"Cefepime/amikacin"	"Cephalosporins (4th gen.)"	"J01DE51,QJ01DE51"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"CPC"	9567559	"Cefepime/clavulanic acid"	"Cephalosporins (4th gen.)"	"J01DE51,QJ01DE51"			"cefcla,cicl,xpml"	"NA"					"NA"
-"FPE"	23653540	"Cefepime/enmetazobactam"	"Cephalosporins (4th gen.)"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
-"FNC"		"Cefepime/nacubactam"	"Cephalosporins (4th gen.)"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
-"FPT"	9567558	"Cefepime/tazobactam"	"Cephalosporins (4th gen.)"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
-"FPZ"		"Cefepime/zidebactam"	"Cephalosporins (4th gen.)"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
-"CAT"	5487888	"Cefetamet"	"Cephalosporins (3rd gen.)"	"J01DD10,QJ01DD10"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefeta,cefmtm"	"cefetametum,deacetoxycefotaxime,epocelin"	1	"g"			"32377-4,35764-0,35765-7,55640-7"
-"CPI"	5486182	"Cefetamet pivoxil"	"Cephalosporins (3rd gen.)"	"NA"			"NA"	"cefetametpivoxil,cefyl,globocef"					"NA"
-"CCL"	71719688	"Cefetecol"	"Cephalosporins (4th gen.)"	"NA"			"cefcatacol"	"NA"					"NA"
-"CZL"	193956	"Cefetrizole"	"Cephalosporins (unclassified gen.)"	"NA"			"NA"	"cefetrizolum"					"NA"
-"FDC"	77843966	"Cefiderocol"	"Cephalosporins (unclassified gen.)"	"J01DI04,QJ01DI04"			"NA"	"fetcroja"			6	"g"	"95767-0,99280-0,99503-5"
-"CFM"	5362065	"Cefixime"	"Cephalosporins (3rd gen.)"	"J01DD08,QJ01DD08"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefixi,cfe,cfix,cfxm,dcfm,fix,ix"	"cefixim,cefixima,cefiximum,cefixoral,cefspan,cephoral,citropen,denvar,necopen,oraken,oroken,suprax,tricef,unixime"	0.4	"g"			"16567-0,18880-5,25236-1,35766-5,79-4,80-2,81-0,82-8"
-"CEO"		"Cefixime/ornidazole"	"Other antibacterials"	"J01DD58,QJ01DD58"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"CMX"	9570757	"Cefmenoxime"	"Cephalosporins (3rd gen.)"	"J01DD05,QJ01DD05,QS01AA31,QS02AA18,S01AA31,S02AA18"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefmen"	"bestron,cefmenoxima,cefmenoximum,tacef"			2	"g"	"32375-8,54174-8,54203-5,55641-5"
-"CMZ"	42008	"Cefmetazole"	"Cephalosporins (2nd gen.)"	"J01DC09,QJ01DC09"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefmet"	"cefmetazol,cefmetazolo,cefmetazolum,cefmetazon,metafar,zefazone"			4	"g"	"11575-8,18881-3,25222-1,87-7,88-5,89-3,90-1"
-"CNX"	71141	"Cefminox"	"Other antibacterials"	"J01DC12,QJ01DC12"			"cefmin"	"alteporina,cefminoxhydrate,cefminoxum,meicelin,tencef"			4	"g"	"54908-9"
-"DIZ"	5361871	"Cefodizime"	"Cephalosporins (3rd gen.)"	"J01DD09,QJ01DD09"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"NA"	"cefodizima,cefodizimum,cefodizme,diezime,kenicef,modivid,neucef,timecef"			2	"g"	"18882-1,6988-0,91-9,92-7,93-5,94-3"
-"CID"	43594	"Cefonicid"	"Cephalosporins (2nd gen.)"	"J01DC06,QJ01DC06"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefoni"	"cefonicide,cefonicido,cefonicidsalt,cefonicidum,monocef,monocid"			1	"g"	"18883-9,25237-9,3444-7,55642-3,95-0,96-8,97-6,98-4"
-"CFP"	44187	"Cefoperazone"	"Cephalosporins (3rd gen.)"	"J01DD12,QJ01DD12,QJ51DD12"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefope,cfp,cfpz,cp,cpz,fop,per"	"bioperazone,cefob,cefobid,cefobis,cefoneg,cefoper,cefoperazin,cefoperazine,cefoperazon,cefoperazona,cefoperazonesalt,cefoperazono,cefoperazonum,cefozon,medocef,myticef,pathozone,peracef,tomabef"			4	"g"	"100-8,101-6,102-4,18884-7,3445-4,35767-3,35768-1,54166-4,54167-2,54168-0,99-2"
-"CSL"		"Cefoperazone/sulbactam"	"Cephalosporins (3rd gen.)"	"J01DD62,QJ01DD62"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"fopsul"	"NA"			4	"g"	"35768-1,54166-4,54167-2,54168-0"
-"CND"	43507	"Ceforanide"	"Cephalosporins (2nd gen.)"	"J01DC11,QJ01DC11"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefora"	"ceforanido,ceforanidum,precef"			4	"g"	"103-2,104-0,105-7,106-5,18885-4,55643-1"
-"CSE"	9830519	"Cefoselis"	"Cephalosporins (4th gen.)"	"NA"			"cefose"	"winsef"					"NA"
-"CTX"	5742673	"Cefotaxime"	"Cephalosporins (3rd gen.)"	"J01DD01,QJ01DD01"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefo32,cefota,cfot,cft,cftx,ct,ctx,fot,fot1,tax,taxmen,taxnme,xct"	"anticefotaxime,cefotax,cefotaxim,cefotaxima,cefotaximesalt,cefotaximsalt,cefotaximum,cephotaxim,cephotaxime,claforan,kefotex,omnatax,pretor,ralopar,tolycar,tolycor,zariviz"			4	"g"	"101479-4,101480-2,107-3,108-1,109-9,110-7,18886-2,25238-7,31138-1,31139-9,3446-2,35769-9,35770-7,35771-5,41671-9,50632-9,52128-6,54191-2,54192-0,54193-8,55189-5,55644-9,6989-8,80961-6"
-"CTX-S"		"Cefotaxime screening test"	"Cephalosporins (3rd gen.)"	"NA"			"ctx screen"	"NA"					"NA"
-"CTC"	9575353	"Cefotaxime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"J01DD51,QJ01DD51"			"cxcl,taxcla,xctl"	"NA"					"NA"
-"CTS"	9574753	"Cefotaxime/sulbactam"	"Cephalosporins (3rd gen.)"	"J01DD51,QJ01DD51"			"NA"	"NA"					"54191-2,54192-0,54193-8,55644-9"
-"CTT"	53025	"Cefotetan"	"Cephalosporins (2nd gen.)"	"J01DC05,QJ01DC05"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefote,cftt,cn,cte,ctn,ctt,tans"	"apacef,apatef,cefotetanum"			4	"g"	"111-5,112-3,113-1,114-9,18887-0,25239-5,3447-0,41672-7,41673-5,41674-3,41729-5,6990-6"
-"CTF"	43708	"Cefotiam"	"Cephalosporins (2nd gen.)"	"J01DC07,QJ01DC07"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefoti"	"aspil,cefotiamum,ceradon,halospor,pansporin,pansporine,spizef"	1.2	"g"	4	"g"	"32374-1,35772-3,35773-1,55645-6,55737-1,55738-9,55739-7,55740-5"
-"CHE"	125846	"Cefotiam hexetil"	"Cephalosporins (3rd gen.)"	"NA"			"NA"	"taketiam,texodil"					"55737-1,55738-9,55739-7,55740-5"
-"FOV"	9578573	"Cefovecin"	"Cephalosporins (3rd gen.)"	"QJ01DD91"			"cefove"	"cefovecinsalt,convenia"					"76147-8,87792-8"
-"FOX"	441199	"Cefoxitin"	"Cephalosporins (2nd gen.)"	"J01DC01,QJ01DC01"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefoxi,cfox,cfx,cfxt,cx,fox,fx"	"betacef,cefoxil,cefoxitina,cefoxitine,cefoxitinsalt,cefoxitinum,cefoxotin,cenomycin,farmoxin,mefoxin,mefoxithin,mefoxitin,merxin,rephoxitin"			6	"g"	"101492-7,115-6,116-4,117-2,118-0,18888-8,25220-5,25240-3,25366-6,3448-8,41675-0,41676-8,41677-6,41730-3,6991-4"
-"FOX-S"		"Cefoxitin screening test"	"Cephalosporins (2nd gen.)"	"NA"			"cfsc,fox1"	"NA"					"NA"
-"ZOP"	9571080	"Cefozopran"	"Cephalosporins (4th gen.)"	"J01DE03,QJ01DE03"			"cefozo"	"firstcin,imidazo"			4	"g"	"100045-4,53820-7"
-"CFZ"	68597	"Cefpimizole"	"Cephalosporins (3rd gen.)"	"NA"			"cefpim"	"ajicef,cefpimizol,cefpimizolesalt,cefpimizolum,renilan"					"NA"
-"CPM"	636405	"Cefpiramide"	"Cephalosporins (3rd gen.)"	"J01DD11,QJ01DD11"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefpam"	"cefpiramida,cefpiramidesalt,cefpiramido,cefpiramidum,sepatren,suncefal"			2	"g"	"NA"
-"CPO"	5479539	"Cefpirome"	"Cephalosporins (4th gen.)"	"J01DE02,QJ01DE02"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"cefpom,cfpr"	"broact,cefir,cefpiroma,cefpiromum,cefrom,keiten,romecef"			4	"g"	"18889-6,6647-3,6648-1,6649-9,6650-6,6992-2,8274-3,8275-0,8276-8"
-"CPD"	6335986	"Cefpodoxime"	"Cephalosporins (3rd gen.)"	"J01DD13,QJ01DD13"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefpod,cfpd,cfpo,cpd,pod,pod4,px"	"cefpodoxima,cefpodoximum,epoxim"	0.4	"g"			"119-8,120-6,121-4,122-2,18890-4,25241-1,41678-4,41679-2,41680-0,41731-1,6993-0,90849-1"
-"CPX"	6526396	"Cefpodoxime proxetil"	"Cephalosporins (3rd gen.)"	"NA"			"NA"	"banan,cefodox,cefoprox,cefpoderm,cefpodoximproxetil,cepodem,doxef,orelox,otreon,podomexef,simplicef,vantin"					"NA"
-"CDC"		"Cefpodoxime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"J01DD64,QJ01DD64"			"cecl,podcla"	"NA"	0.4	"g"			"NA"
-"CPR"	5281006	"Cefprozil"	"Cephalosporins (2nd gen.)"	"J01DC10,QJ01DC10"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefpro,cpr,cpz,fp"	"arzimol,brisoral,cefprozilo,cefprozilum,cronocef,procef,serozil"	1	"g"			"123-0,124-8,125-5,126-3,18891-2,6994-8"
-"CEQ"	5464355	"Cefquinome"	"Cephalosporins (4th gen.)"	"QG51AA07,QJ01DE90,QJ51DE90"			"cefqui"	"cefquinoma,cefquinomum,cobactan,quinolinium"					"100046-2,76150-2"
-"CRD"	5284529	"Cefroxadine"	"Cephalosporins (1st gen.)"	"J01DB11,QJ01DB11"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"ceftix"	"cefroxadin,cefroxadino,cefroxadinum,oraspor"	2.1	"g"			"NA"
-"CFS"	656575	"Cefsulodin"	"Cephalosporins (3rd gen.)"	"J01DD03,QJ01DD03"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefsul,cfsl,cfsu"	"cefomonil,cefonomil,cefsulodine,cefsulodinhydrate,cefsulodino,cefsulodinum,pseudocef,pseudomonil,pyocefal,sulcephalosporin,takesulin,tilmapor,ulfaret"			4	"g"	"127-1,128-9,129-7,130-5,131-3,18892-0,25242-9,55647-2"
-"CSU"	68718	"Cefsumide"	"Cephalosporins (unclassified gen.)"	"NA"			"NA"	"cefsulmid,cefsumido,cefsumidum"					"NA"
-"CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"	"J01DI02,QJ01DI02"			"ceftar,cfro"	"ceftaroine,teflaro,zinforo"					"73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
-"CPA"		"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"	"NA"			"NA"	"NA"					"73604-1,73626-4,73649-6"
-"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02,QJ01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cefta,ceftaz,cfta,cftz,taz,tz,xtz"	"ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime"			4	"g"	"101481-0,101482-8,101483-6,132-1,133-9,134-7,135-4,18893-8,21151-6,3449-6,35774-9,35775-6,35776-4,42352-5,55648-0,55649-8,55650-6,55651-4,58705-5,6995-5,73603-3,73625-6,73648-8,80960-8,87734-0,90850-9"
-"CZA"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"	"J01DD52,QJ01DD52"			"cfav"	"avycaz,zavicefta"			6	"g"	"101483-6,73603-3,73625-6,73648-8,87734-0"
-"CCV"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"J01DD52,QJ01DD52"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"czcl,tazcla,xtzl"	"NA"			6	"g"	"NA"
-"CEM"	6537431	"Cefteram"	"Cephalosporins (3rd gen.)"	"J01DD18,QJ01DD18"			"cefter"	"cefterame,cefteramum,ceftetrame"	0.4	"g"			"100047-0,76144-5"
-"CPL"	5362114	"Cefteram pivoxil"	"Cephalosporins (3rd gen.)"	"NA"			"NA"	"cefterampivoxil,tomiron"					"NA"
-"CTL"	65755	"Ceftezole"	"Cephalosporins (1st gen.)"	"J01DB12,QJ01DB12"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"ceftez"	"alomen,ceftezol,ceftezolesalt,ceftezolo,ceftezolum,celoslin,demethylcefazolin,falomesin"			3	"g"	"NA"
-"CTB"	5282242	"Ceftibuten"	"Cephalosporins (3rd gen.)"	"J01DD14,QJ01DD14"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cb,ceftib,cfbu,ctb,tib"	"cedax,ceftem,ceftibutene,ceftibuteno,ceftibutenum,ceftibutin,ceprifran,isocef,keimax,seftem"	0.4	"g"			"35777-2,35778-0,35779-8,6996-3"
-"TIO"	6328657	"Ceftiofur"	"Cephalosporins (3rd gen.)"	"QJ01DD90,QJ51DD90"			"ceftif"	"ceftiofurum,excenel,naxcel"					"23709-9,35780-6,35781-4,55652-2"
-"CZX"	6533629	"Ceftizoxime"	"Cephalosporins (3rd gen.)"	"J01DD07,QJ01DD07"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"ceftiz,cfzx,ctz,cz,czx,tiz,zox"	"cefizox,ceftix,ceftizoxima,ceftizoximesalt,ceftizoximum,eposerin"			4	"g"	"136-2,137-0,138-8,139-6,18894-6,20378-6,23622-4,25243-7,3450-4,6997-1"
-"CZP"	9578661	"Ceftizoxime alapivoxil"	"Cephalosporins (3rd gen.)"	"NA"			"NA"	"NA"					"NA"
-"BPR"	135413542	"Ceftobiprole"	"Cephalosporins (5th gen.)"	"NA"			"ceftob"	"NA"					"43269-0,43270-8,43271-6,43272-4,85052-9"
-"CFM1"	135413544	"Ceftobiprole medocaril"	"Cephalosporins (5th gen.)"	"J01DI01,QJ01DI01"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	"NA"	"zevtera"			1.5	"g"	"NA"
-"CZT"	86291594	"Ceftolozane/tazobactam"	"Cephalosporins (5th gen.)"	"J01DI54,QJ01DI54"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	"cei"	"zerbaxa"			3	"g"	"101484-4,73602-5,73624-9,73647-0,87735-7"
-"CRO"	5479530	"Ceftriaxone"	"Cephalosporins (3rd gen.)"	"J01DD04,QJ01DD04"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"axo,cax,ceftri,cftr,cro,ctr,frx,trimen,trinme,tx"	"biotrakson,ceftriaxon,ceftriaxona,ceftriaxonum,ceftriazone,rocefin,rocephalin,rocephin,rocephine,rophex"			2	"g"	"101485-1,140-4,141-2,142-0,143-8,18895-3,25244-5,25367-4,31140-7,31141-5,3451-2,41681-8,41682-6,41683-4,41732-9,50633-7,55190-3,6998-9,80957-4"
-"CEB"		"Ceftriaxone/beta-lactamase inhibitor"	"Cephalosporins (3rd gen.)"	"J01DD63,QJ01DD63"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"NA"	"NA"			2	"g"	"NA"
-"CXM"	5479529	"Cefuroxime"	"Cephalosporins (2nd gen.)"	"J01DC02,QJ01DC02,QJ51DC02,QS01AA27,S01AA27"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefaxe,cefrox,cefuro,cfrx,cfur,cfx,crm,cxm,fur,rox,xm"	"anaptivan,biociclin,biofuroksym,bioxima,cefofix,cefumax,cefurex,cefuril,cefurox,cefuroxim,cefuroxima,cefuroximesalt,cefuroximine,cefuroximo,cefuroximum,cephuroxime,cetroxil,colifossim,curoxim,curoxima,curoxime,froxal,furoxil,kefurox,kesint,ketocef,lifurox,medoxim,sharox,spectrazolr,ultroxim,zinacef,zinnat"	0.5	"g"	3	"g"	"101503-1,144-6,145-3,146-1,147-9,18896-1,20460-2,25245-2,3452-0,35782-2,35783-0,51724-3,51774-8,55653-0,55654-8,6999-7,74699-0,80608-3,80617-4"
-"CXA"	6321416	"Cefuroxime axetil"	"Cephalosporins (2nd gen.)"	"NA"			"cfax"	"bioracef,ceftin,cefurax,cefuroximaxetil,celocid,cepazine,cethixim,cetoxil,coliofossim,curocef,elobact,kalcef,maxitil,medoxm,nivador,novador,novocef,oraxim,zinat,zoref"					"NA"
-"CFM2"		"Cefuroxime/metronidazole"	"Other antibacterials"	"J01DC52,QJ01DC52"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"	0.5	"g"			"NA"
-"ZON"	6336505	"Cefuzonam"	"Other antibacterials"	"NA"			"cefuzo"	"cefuzoname,cefuzonamum,cefzoname,cosmosin"					"NA"
-"CED"	38103	"Cephradine"	"Cephalosporins (1st gen.)"	"NA"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cephra,cfra,cfrd"	"anspor,cefradin,cefradina,cefradine,cefradinum,cekodin,cephradin,ecosporina,eskacef,infexin,megacef,sefril,velocef,velosef"					"168-5,169-3,170-1,171-9,18902-7,55646-4"
+"CRB"	20824	"Carbenicillin"	"Penicillins,Beta-lactams"	"J01CA03,QJ01CA03"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"bar,carb,carben,cb"	"anabactyl,carbecin,carbenicilina,carbenicillina,carbenicilline,carbenicillinum,dicarbenicillin,dipenicillin,fugacillin,geopen,gripenin,hyoper,microcillin,piopen,pyocianil,pyoclox,pyopan,pyopen,pyopene"			12	"g"	"18873-0,3434-8,41668-5,59-6,60-4,61-2,62-0"
+"CRN"	93184	"Carindacillin"	"Penicillins,Beta-lactams"	"J01CA05,QJ01CA05"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"carindacilina,carindacilline,carindacillinsalt,carindacillinum,geocillin,indanylcarbinicillin,urobac"	4	"g"			"NA"
+"CAR"	6540466	"Carumonam"	"Monobactams,Beta-lactams"	"J01DF02,QJ01DF02"			"NA"	"carumonamum"			2	"g"	"51694-8"
+"CAS"	2826718	"Caspofungin"	"Antifungals"	"J02AX04,QJ02AX04"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"casp,caspof"	"cancidas,caspofungina"			50	"mg"	"32378-2,54175-5,54176-3,54185-4,58419-3"
+"CAC"	91562	"Cefacetrile"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB10,QJ01DB10,QJ51DB10"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cephac"	"cefacetril,cefacetrilo,cefacetrilum,celospor,cephacetrile,vetrimast"					"55624-1,55625-8,55626-6,55627-4"
+"CEC"	51039	"Cefaclor"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC04,QJ01DC04"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"ccl,cec,cefacl,cf,cfac,cfc,cfcl,cfr,fac"	"alenfral,alfacet,alfatil,ceclor,cefachlor,cefaclorum,cefeaclor,cephaclor,compound,distaclor,keflor,kefolor,kefral,keftab,keftid,lilly,lopac,panacef,panoral,raniclor"	1	"g"			"16564-7,18874-8,21149-0,6986-4,83-6,84-4,85-1,86-9"
+"CFR"	47965	"Cefadroxil"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB05,QJ01DB05"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefadr,cfdx,cfr,fad"	"bidocel,cefadrops,cefadroxilo,cefadroxilum,cefradroxil,cefzil,cephadroxil,duracef,duricef,kefroxil,sumacef,ultracef"	2	"g"			"16565-4,18875-5,55628-2,63-8,64-6,65-3,66-1"
+"LEX"	27447	"Cefalexin"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB01,QJ01DB01,QJ51DB01"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cepale,cflx"	"adcadina,alcephin,alsporin,ambal,amplex,aristosporin,azabort,bactopenor,beliam,biocef,carnosporin,cefablan,cefacet,cefadal,cefadin,cefadina,cefalekey,cefaleksin,cefalessina,cefalexgobens,cefalexina,cefalexine,cefalexinum,cefalin,cefalival,cefaloto,cefanex,cefaseptin,cefax,ceffanex,cefibacter,ceflax,ceforal,cefovit,celexin,cepastar,cepexin,cephacillin,cephalexine,cephalexinum,cephalobene,cephanasten,cephaxin,cephin,cepol,ceporex,ceporexin,ceporexine,cerexin,cerexins,check,cophalexin,domucef,doriman,durantel,efemida,erocetin,factagard,felexin,fexin,ibilex,ibrexin,inphalex,karilexina,kefalospes,keflet,keflex,kefolan,keforal,kekrinal,kidolex,lafarine,larixin,lenocef,lexibiotico,loisine,lonflex,lopilexin,losporal,madlexin,maksipor,mamalexin,mamlexin,medolexin,medoxine,neokef,neolexina,noveol,novolexin,nufex,optocef,oracef,oriphex,oroxin,ortisporina,ospexin,palitrex,panixine,pectril,prindex,pyassan,rilexine,roceph,rogevil,sanaxin,sartosona,sencephalin,sepexin,servicef,servispor,sialexin,sinthecillin,sintolexyn,sporicef,sporidex,syncl,syncle,synecl,taicelexin,tepaxin,theratrex,tokiolexin,uphalexin,viosporine,voxxim,winlex,zabytrex,zozarine"	2	"g"			"NA"
+"RID"	5773	"Cefaloridine"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB02,QJ01DB02"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefa,ceplor"	"aliporina,ampligram,cefaloridin,cefaloridina,cefaloridinum,cefalorizin,ceflorin,cepaloridin,cepalorin,cephalomycine,cephaloridin,cephaloridine,cephaloridinum,ceporan,ceporin,ceporine,cilifor,deflorin,faredina,floridin,glaxoridin,intrasporin,keflodin,keflordin,kefloridin,kefspor,lloncefal,sasperin,sefacin,verolgin,vioviantine"			3	"g"	"NA"
+"CEP"	6024	"Cefalotin"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB03,QJ01DB03"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cephal,cfal,cflt"	"averon,cefalothin,cefalothine,cefalothinsalt,cefalotina,cefalotine,cefalotinsalt,cefalotinum,cemastin,cephalothin,cephalothinsalt,cephalothinum,cephalotin,cephalotinsalt,ceporacin,cepovenin,coaxin,keflin,lospoven,microtin,seffin,synclotin,toricelocin"			4	"g"	"NA"
+"MAN"	456255	"Cefamandole"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC03,QJ01DC03"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefama,cfam,cfmn"	"cefadole,cefamandol,cefamandolum,cephadole,kefamandol,kefdole,mancef"			6	"g"	"18876-3,3441-3,41669-3,55634-0,55635-7,55636-5,55637-3,67-9,68-7,69-5,70-3"
+"HAP"	30699	"Cefapirin"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB08,QG51AA05,QJ01DB08,QJ51DB08"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cephap"	"ambrocef,brisfirina,brisporin,bristocef,cefadyl,cefalak,cefaloject,cefapirina,cefapirine,cefapirinsalt,cefapirinum,cefaprin,cefatrex,cefatrexyl,cephapirin,cephapirine,cephapirinsalt,cephatrexil,cephatrexyl,metricure"			4	"g"	"NA"
+"CTZ"	6410758	"Cefatrizine"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB07,QJ01DB07"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefatr"	"bricef,cefathiamidine,cefatrix,cefatrizino,cefatrizinum,cephatriazine,cepticol,cetrazil,latocef,orosporina,orotric,seapuron,trizina"	1	"g"			"18877-1,55639-9,71-1,72-9,73-7,74-5"
+"CZD"	71736	"Cefazedone"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB06,QJ01DB06"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefaze"	"cefazedon,cefazedona,cefazedonesalt,cefazedonum,refosporen,refosporene,refosporin,refosporinsalt"			3	"g"	"NA"
+"CZO"	33255	"Cefazolin"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB04,QJ01DB04,QJ51DB04"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefazo,cfz,cfzl,cz,czol,faz,kz"	"ancef,atirin,biazolina,cefabiozim,cefacidal,cefalomicina,cefamedin,cefamezin,cefazil,cefazina,cefazolina,cefazoline,cefazolinsalt,cefazolinum,cephamezine,cephazolidin,cephazolin,cephazoline,elzogram,firmacef,gramaxin,kefzol,lampocef,liviclina,neofazol,oprea,recef,totacef,zolicef,zolisint"			3	"g"	"16566-2,18878-9,25235-3,3442-1,3443-9,41670-1,75-2,76-0,77-8,78-6,80962-4,85422-4"
+"CFB"	127527	"Cefbuperazone"	"Other"	"J01DC13,QJ01DC13"			"cefbup"	"cefbuperazona,cefbuperazonesalt,cefbuperazonum,cefbuperzaone,cerbuperazone,keiperazon,tomiporan"			2	"g"	"NA"
+"CCP"	6436055	"Cefcapene"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD17,QJ01DD17"			"cefcap"	"flomox"	0.45	"g"			"100044-7,76143-7"
+"CCX"	5282438	"Cefcapene pivoxil"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"NA"	"cefcamate,flumax"					"NA"
+"CDR"	6915944	"Cefdinir"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD15,QJ01DD15"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cd,cdn,cdr,cefdin,cfd,din"	"cefdinirum,cefdinyl,cefdirnir,ceftinex,cefzon,omnicef"	0.6	"g"			"23636-4,23637-2,35757-4,35758-2"
+"DIT"	9870843	"Cefditoren"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD16,QJ01DD16"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cdn,cefdit"	"cefditoreno,spectracef"	0.4	"g"			"35759-0,35760-8,35761-6,35762-4"
+"DIX"	6437877	"Cefditoren pivoxil"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"NA"	"cefditorin,meiact,pivaloyloxymethyl"					"NA"
+"FEP"	5479537	"Cefepime"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams"	"J01DE01,QJ01DE01"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"cefep4,cefepi,cfep,cfpi,cpe,cpm,fep,pm,xpm"	"anticefepime,axepim,cefepima,cefepimum,maxipime,pyrrolidinium,renapime"			4	"g"	"101502-3,18879-7,31142-3,31143-1,35763-2,38363-8,42350-9,42351-7,42353-3,50631-1,58412-8,6643-1,6644-9,6645-7,6646-5,6987-2,8272-7,8273-5"
+"CFA"		"Cefepime/amikacin"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams"	"J01DE51,QJ01DE51"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"CPC"	9567559	"Cefepime/clavulanic acid"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams"	"J01DE51,QJ01DE51"			"cefcla,cicl,xpml"	"NA"					"NA"
+"FPE"	23653540	"Cefepime/enmetazobactam"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
+"FNC"		"Cefepime/nacubactam"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
+"FTA"		"Cefepime/taniborbactam"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
+"FPT"	9567558	"Cefepime/tazobactam"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
+"FPZ"		"Cefepime/zidebactam"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DE51,QJ01DE51"			"NA"	"NA"					"NA"
+"CAT"	5487888	"Cefetamet"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD10,QJ01DD10"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefeta,cefmtm"	"cefetametum,deacetoxycefotaxime,epocelin"	1	"g"			"32377-4,35764-0,35765-7,55640-7"
+"CPI"	5486182	"Cefetamet pivoxil"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"NA"	"cefetametpivoxil,cefyl,globocef"					"NA"
+"CCL"	71719688	"Cefetecol"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams"	"NA"			"cefcatacol"	"NA"					"NA"
+"CZL"	193956	"Cefetrizole"	"Cephalosporins,Beta-lactams"	"NA"			"NA"	"cefetrizolum"					"NA"
+"FDC"	77843966	"Cefiderocol"	"Cephalosporins,Beta-lactams"	"J01DI04,QJ01DI04"			"NA"	"fetcroja"			6	"g"	"95767-0,99280-0,99503-5"
+"CFM"	5362065	"Cefixime"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD08,QJ01DD08"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefixi,cfe,cfix,cfxm,dcfm,fix,ix"	"cefixim,cefixima,cefiximum,cefixoral,cefspan,cephoral,citropen,denvar,necopen,oraken,oroken,suprax,tricef,unixime"	0.4	"g"			"16567-0,18880-5,25236-1,35766-5,79-4,80-2,81-0,82-8"
+"CEO"		"Cefixime/ornidazole"	"Other"	"J01DD58,QJ01DD58"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"CMX"	9570757	"Cefmenoxime"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD05,QJ01DD05,QS01AA31,QS02AA18,S01AA31,S02AA18"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefmen"	"bestron,cefmenoxima,cefmenoximum,tacef"			2	"g"	"32375-8,54174-8,54203-5,55641-5"
+"CMZ"	42008	"Cefmetazole"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC09,QJ01DC09"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefmet"	"cefmetazol,cefmetazolo,cefmetazolum,cefmetazon,metafar,zefazone"			4	"g"	"11575-8,18881-3,25222-1,87-7,88-5,89-3,90-1"
+"CNX"	71141	"Cefminox"	"Other"	"J01DC12,QJ01DC12"			"cefmin"	"alteporina,cefminoxhydrate,cefminoxum,meicelin,tencef"			4	"g"	"54908-9"
+"DIZ"	5361871	"Cefodizime"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD09,QJ01DD09"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"NA"	"cefodizima,cefodizimum,cefodizme,diezime,kenicef,modivid,neucef,timecef"			2	"g"	"18882-1,6988-0,91-9,92-7,93-5,94-3"
+"CID"	43594	"Cefonicid"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC06,QJ01DC06"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefoni"	"cefonicide,cefonicido,cefonicidsalt,cefonicidum,monocef,monocid"			1	"g"	"18883-9,25237-9,3444-7,55642-3,95-0,96-8,97-6,98-4"
+"CFP"	44187	"Cefoperazone"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD12,QJ01DD12,QJ51DD12"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefope,cfp,cfpz,cp,cpz,fop,per"	"bioperazone,cefob,cefobid,cefobis,cefoneg,cefoper,cefoperazin,cefoperazine,cefoperazon,cefoperazona,cefoperazonesalt,cefoperazono,cefoperazonum,cefozon,medocef,myticef,pathozone,peracef,tomabef"			4	"g"	"100-8,101-6,102-4,18884-7,3445-4,35767-3,35768-1,54166-4,54167-2,54168-0,99-2"
+"CSL"		"Cefoperazone/sulbactam"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DD62,QJ01DD62"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"fopsul"	"NA"			4	"g"	"35768-1,54166-4,54167-2,54168-0"
+"CND"	43507	"Ceforanide"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC11,QJ01DC11"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefora"	"ceforanido,ceforanidum,precef"			4	"g"	"103-2,104-0,105-7,106-5,18885-4,55643-1"
+"CSE"	9830519	"Cefoselis"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams"	"NA"			"cefose"	"winsef"					"NA"
+"CTX"	5742673	"Cefotaxime"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD01,QJ01DD01"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefo32,cefota,cfot,cft,cftx,ct,ctx,fot,fot1,tax,taxmen,taxnme,xct"	"anticefotaxime,cefotax,cefotaxim,cefotaxima,cefotaximesalt,cefotaximsalt,cefotaximum,cephotaxim,cephotaxime,claforan,kefotex,omnatax,pretor,ralopar,tolycar,tolycor,zariviz"			4	"g"	"101479-4,101480-2,107-3,108-1,109-9,110-7,18886-2,25238-7,31138-1,31139-9,3446-2,35769-9,35770-7,35771-5,41671-9,50632-9,52128-6,54191-2,54192-0,54193-8,55189-5,55644-9,6989-8,80961-6"
+"CTX-S"		"Cefotaxime screening test"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"ctx screen"	"NA"					"NA"
+"CTC"	9575353	"Cefotaxime/clavulanic acid"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD51,QJ01DD51"			"cxcl,taxcla,xctl"	"NA"					"NA"
+"CTS"	9574753	"Cefotaxime/sulbactam"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DD51,QJ01DD51"			"NA"	"NA"					"54191-2,54192-0,54193-8,55644-9"
+"CTT"	53025	"Cefotetan"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC05,QJ01DC05"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefote,cftt,cn,cte,ctn,ctt,tans"	"apacef,apatef,cefotetanum"			4	"g"	"111-5,112-3,113-1,114-9,18887-0,25239-5,3447-0,41672-7,41673-5,41674-3,41729-5,6990-6"
+"CTF"	43708	"Cefotiam"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC07,QJ01DC07"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefoti"	"aspil,cefotiamum,ceradon,halospor,pansporin,pansporine,spizef"	1.2	"g"	4	"g"	"32374-1,35772-3,35773-1,55645-6,55737-1,55738-9,55739-7,55740-5"
+"CHE"	125846	"Cefotiam hexetil"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"NA"	"taketiam,texodil"					"55737-1,55738-9,55739-7,55740-5"
+"FOV"	9578573	"Cefovecin"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"QJ01DD91"			"cefove"	"cefovecinsalt,convenia"					"76147-8,87792-8"
+"FOX"	441199	"Cefoxitin"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC01,QJ01DC01"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefoxi,cfox,cfx,cfxt,cx,fox,fx"	"betacef,cefoxil,cefoxitina,cefoxitine,cefoxitinsalt,cefoxitinum,cefoxotin,cenomycin,farmoxin,mefoxin,mefoxithin,mefoxitin,merxin,rephoxitin"			6	"g"	"101492-7,115-6,116-4,117-2,118-0,18888-8,25220-5,25240-3,25366-6,3448-8,41675-0,41676-8,41677-6,41730-3,6991-4"
+"FOX-S"		"Cefoxitin screening test"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"NA"			"cfsc,fox1"	"NA"					"NA"
+"ZOP"	9571080	"Cefozopran"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams"	"J01DE03,QJ01DE03"			"cefozo"	"firstcin,imidazo"			4	"g"	"100045-4,53820-7"
+"CFZ"	68597	"Cefpimizole"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"cefpim"	"ajicef,cefpimizol,cefpimizolesalt,cefpimizolum,renilan"					"NA"
+"CPM"	636405	"Cefpiramide"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD11,QJ01DD11"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefpam"	"cefpiramida,cefpiramidesalt,cefpiramido,cefpiramidum,sepatren,suncefal"			2	"g"	"NA"
+"CPO"	5479539	"Cefpirome"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams"	"J01DE02,QJ01DE02"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"cefpom,cfpr"	"broact,cefir,cefpiroma,cefpiromum,cefrom,keiten,romecef"			4	"g"	"18889-6,6647-3,6648-1,6649-9,6650-6,6992-2,8274-3,8275-0,8276-8"
+"CPD"	6335986	"Cefpodoxime"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD13,QJ01DD13"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefpod,cfpd,cfpo,cpd,pod,pod4,px"	"cefpodoxima,cefpodoximum,epoxim"	0.4	"g"			"119-8,120-6,121-4,122-2,18890-4,25241-1,41678-4,41679-2,41680-0,41731-1,6993-0,90849-1"
+"CPX"	6526396	"Cefpodoxime proxetil"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"NA"	"banan,cefodox,cefoprox,cefpoderm,cefpodoximproxetil,cepodem,doxef,orelox,otreon,podomexef,simplicef,vantin"					"NA"
+"CDC"		"Cefpodoxime/clavulanic acid"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD64,QJ01DD64"			"cecl,podcla"	"NA"	0.4	"g"			"NA"
+"CPR"	5281006	"Cefprozil"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC10,QJ01DC10"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefpro,cpr,cpz,fp"	"arzimol,brisoral,cefprozilo,cefprozilum,cronocef,procef,serozil"	1	"g"			"123-0,124-8,125-5,126-3,18891-2,6994-8"
+"CEQ"	5464355	"Cefquinome"	"Cephalosporins (4th gen.),Cephalosporins,Beta-lactams"	"QG51AA07,QJ01DE90,QJ51DE90"			"cefqui"	"cefquinoma,cefquinomum,cobactan,quinolinium"					"100046-2,76150-2"
+"CRD"	5284529	"Cefroxadine"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB11,QJ01DB11"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"ceftix"	"cefroxadin,cefroxadino,cefroxadinum,oraspor"	2.1	"g"			"NA"
+"CFS"	656575	"Cefsulodin"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD03,QJ01DD03"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefsul,cfsl,cfsu"	"cefomonil,cefonomil,cefsulodine,cefsulodinhydrate,cefsulodino,cefsulodinum,pseudocef,pseudomonil,pyocefal,sulcephalosporin,takesulin,tilmapor,ulfaret"			4	"g"	"127-1,128-9,129-7,130-5,131-3,18892-0,25242-9,55647-2"
+"CSU"	68718	"Cefsumide"	"Cephalosporins,Beta-lactams"	"NA"			"NA"	"cefsulmid,cefsumido,cefsumidum"					"NA"
+"CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.),Cephalosporins,Beta-lactams"	"J01DI02,QJ01DI02"			"ceftar,cfro"	"ceftaroine,teflaro,zinforo"					"73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
+"CPA"		"Ceftaroline/avibactam"	"Cephalosporins (5th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"NA"	"NA"					"73604-1,73626-4,73649-6"
+"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD02,QJ01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cef,cefta,ceftaz,cfta,cftz,taz,tz,xtz"	"ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime"			4	"g"	"101481-0,101482-8,101483-6,132-1,133-9,134-7,135-4,18893-8,21151-6,3449-6,35774-9,35775-6,35776-4,42352-5,55648-0,55649-8,55650-6,55651-4,58705-5,6995-5,73603-3,73625-6,73648-8,80960-8,87734-0,90850-9"
+"CZA"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DD52,QJ01DD52"			"cfav"	"avycaz,zavicefta"			6	"g"	"101483-6,73603-3,73625-6,73648-8,87734-0"
+"CCV"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD52,QJ01DD52"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"czcl,tazcla,xtzl"	"NA"			6	"g"	"NA"
+"CEM"	6537431	"Cefteram"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD18,QJ01DD18"			"cefter"	"cefterame,cefteramum,ceftetrame"	0.4	"g"			"100047-0,76144-5"
+"CPL"	5362114	"Cefteram pivoxil"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"NA"	"cefterampivoxil,tomiron"					"NA"
+"CTL"	65755	"Ceftezole"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"J01DB12,QJ01DB12"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"ceftez"	"alomen,ceftezol,ceftezolesalt,ceftezolo,ceftezolum,celoslin,demethylcefazolin,falomesin"			3	"g"	"NA"
+"CTB"	5282242	"Ceftibuten"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD14,QJ01DD14"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cb,ceftib,cfbu,ctb,tib"	"cedax,ceftem,ceftibutene,ceftibuteno,ceftibutenum,ceftibutin,ceprifran,isocef,keimax,seftem"	0.4	"g"			"35777-2,35778-0,35779-8,6996-3"
+"TIO"	6328657	"Ceftiofur"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"QJ01DD90,QJ51DD90"			"ceftif"	"ceftiofurum,excenel,naxcel"					"23709-9,35780-6,35781-4,55652-2"
+"CZX"	6533629	"Ceftizoxime"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD07,QJ01DD07"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"ceftiz,cfzx,ctz,cz,czx,tiz,zox"	"cefizox,ceftix,ceftizoxima,ceftizoximesalt,ceftizoximum,eposerin"			4	"g"	"136-2,137-0,138-8,139-6,18894-6,20378-6,23622-4,25243-7,3450-4,6997-1"
+"CZP"	9578661	"Ceftizoxime alapivoxil"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"NA"			"NA"	"NA"					"NA"
+"BPR"	135413542	"Ceftobiprole"	"Cephalosporins (5th gen.),Cephalosporins,Beta-lactams"	"NA"			"ceftob"	"NA"					"43269-0,43270-8,43271-6,43272-4,85052-9"
+"CFM1"	135413544	"Ceftobiprole medocaril"	"Cephalosporins (5th gen.),Cephalosporins,Beta-lactams"	"J01DI01,QJ01DI01"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	"NA"	"zevtera"			1.5	"g"	"NA"
+"CZT"	86291594	"Ceftolozane/tazobactam"	"Cephalosporins (5th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors"	"J01DI54,QJ01DI54"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	"cei"	"zerbaxa"			3	"g"	"101484-4,73602-5,73624-9,73647-0,87735-7"
+"CRO"	5479530	"Ceftriaxone"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD04,QJ01DD04"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"axo,cax,ceftri,cftr,cro,ctr,frx,trimen,trinme,tx"	"biotrakson,ceftriaxon,ceftriaxona,ceftriaxonum,ceftriazone,rocefin,rocephalin,rocephin,rocephine,rophex"			2	"g"	"101485-1,140-4,141-2,142-0,143-8,18895-3,25244-5,25367-4,31140-7,31141-5,3451-2,41681-8,41682-6,41683-4,41732-9,50633-7,55190-3,6998-9,80957-4"
+"CEB"		"Ceftriaxone/beta-lactamase inhibitor"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD63,QJ01DD63"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"NA"	"NA"			2	"g"	"NA"
+"CXM"	5479529	"Cefuroxime"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC02,QJ01DC02,QJ51DC02,QS01AA27,S01AA27"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cefaxe,cefrox,cefuro,cfrx,cfur,cfx,crm,cxm,fur,rox,xm"	"anaptivan,biociclin,biofuroksym,bioxima,cefofix,cefumax,cefurex,cefuril,cefurox,cefuroxim,cefuroxima,cefuroximesalt,cefuroximine,cefuroximo,cefuroximum,cephuroxime,cetroxil,colifossim,curoxim,curoxima,curoxime,froxal,furoxil,kefurox,kesint,ketocef,lifurox,medoxim,sharox,spectrazolr,ultroxim,zinacef,zinnat"	0.5	"g"	3	"g"	"101503-1,144-6,145-3,146-1,147-9,18896-1,20460-2,25245-2,3452-0,35782-2,35783-0,51724-3,51774-8,55653-0,55654-8,6999-7,74699-0,80608-3,80617-4"
+"CXA"	6321416	"Cefuroxime axetil"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"NA"			"cfax"	"bioracef,ceftin,cefurax,cefuroximaxetil,celocid,cepazine,cethixim,cetoxil,coliofossim,curocef,elobact,kalcef,maxitil,medoxm,nivador,novador,novocef,oraxim,zinat,zoref"					"NA"
+"CFM2"		"Cefuroxime/metronidazole"	"Other"	"J01DC52,QJ01DC52"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"	0.5	"g"			"NA"
+"ZON"	6336505	"Cefuzonam"	"Other"	"NA"			"cefuzo"	"cefuzoname,cefuzonamum,cefzoname,cosmosin"					"NA"
+"CED"	38103	"Cephradine"	"Cephalosporins (1st gen.),Cephalosporins,Beta-lactams"	"NA"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cephra,cfra,cfrd"	"anspor,cefradin,cefradina,cefradine,cefradinum,cekodin,cephradin,ecosporina,eskacef,infexin,megacef,sefril,velocef,velosef"					"168-5,169-3,170-1,171-9,18902-7,55646-4"
 "CTO"	71402	"Cetocycline"	"Tetracyclines"	"NA"			"NA"	"cetocyline,cetotetrine,chelocardin"					"NA"
 "CHL"	5959	"Chloramphenicol"	"Phenicols"	"D06AX02,D10AF03,G01AA05,J01BA01,QD06AX02,QD10AF03,QG01AA05,QJ01BA01,QJ51BA01,QS01AA01,QS02AA01,QS03AA08,S01AA01,S02AA01,S03AA08"	"Amphenicols"	"Amphenicols"	"c,chl,chlo,chlora,cl"	"alficetyn,ambofen,amphicol,amseclor,anacetin,aquamycetin,austracil,austracol,biocetin,biophenicol,catilan,chemicetin,chemicetina,chlomin,chlomycol,chloramex,chloramfenikol,chloramficin,chloramfilin,chloramphenicole,chloramphenicolum,chloramsaar,chlorasol,chlorbiotic,chloricol,chlornitromycin,chloroamphenicol,chlorocaps,chlorocid,chlorocide,chlorocin,chlorocol,chlorofair,chloromax,chloromycetin,chloromycetny,chloromyxin,chloronitrin,chloroptic,chlorovules,cidocetine,ciplamycetin,cloramfen,cloramfenicol,cloramfenicolo,cloramficin,cloramicol,cloramidina,cloranfenicol,cloroamfenicolo,clorocyn,cloromisan,clorosintex,comycetin,cylphenicol,desphen,detreomycin,detreomycine,dextramycin,dextromycetin,doctamicina,econochlor,embacetin,emetren,enteromycetin,erbaplast,ertilen,farmicetina,globenicol,glorous,gloveticol,halcetin,halomycetin,hortfenicol,intramycetin,isicetin,ismicetina,isophenicol,juvamycetin,kamaver,kemicetina,kemicetine,kloramfenikol,klorita,laevomycetinum,leukamycin,leukomyan,leukomycin,levocin,levomicetina,levomitsetin,levomycetin,levoplast,levosin,levovetin,loromisan,loromisin,mastiphen,maybridge,mediamycetine,medichol,micloretin,micochlorine,micoclorina,microcetina,mychel,mycinol,myclocin,mycochlorin,novochlorocap,novomycetin,novophenicol,ocuphenicol,oftalent,oleomycetin,opclor,opelor,ophthochlor,ophthocort,ophtochlor,optomycin,otachron,otophen,pantovernil,paraxin,pentamycetin,petnamycetin,quemicetina,rivomycin,romphenil,ronphenil,septicol,sificetina,sintomicetin,sintomicetina,soluthor,stanomycetin,synthomycetin,synthomycetine,synthomycine,syntomycin,tevcocin,tevcosin,tifomycin,tifomycine,tiromycetin,treomicetina,tyfomycine,unimycetin,veticol,viceton"	3	"g"	3	"g"	"15101-9,16603-3,16604-1,172-7,173-5,174-3,175-0,18903-5,25247-8,29214-4,29346-4,29347-2,3455-3,7001-1"
 "CTE"	54675777	"Chlortetracycline"	"Tetracyclines"	"A01AB21,D06AA02,J01AA03,QA01AB21,QD06AA02,QG51AA08,QJ01AA03,QJ51AA03,QS01AA02,S01AA02"	"Tetracyclines"	"Tetracyclines"	"chltet"	"acronize,alexomycin,aueromycin,aureocarmyl,aureociclina,aureocina,aureocycline,aureomycin,aureomykoin,aurofac,auxeomycin,biomitsin,biomycin,chlormax,chlorotetracycline,chlortetracyclinum,chrysomykine,clorocipan,clortetraciclina,clortetrin,declomycin,declostatin,deganol,demeclor,demeplus,demetraciclina,demetraclin,detracin,detravis,diuciclin,duomycin,elkamicina,flamycin,isphamycin,ledermicina,ledermycin,ledermycine,mexocine,novotriclina,pennchlor,perciclina,periciclina,sumaclina,uromycin,veraciclina"	1	"g"			"176-8,177-6,178-4,179-2,18904-3,55655-5,87600-3"
-"CIC"	19003	"Ciclacillin"	"Beta-lactams/penicillins"	"NA"			"cyclac"	"bastcillin,calthor,ciclacilina,ciclacilline,ciclacillinum,ciclacillum,citosarin,cyclacillin,cyclapen,noblicil,orfilina,peamezin,syngacillin,ultracillin,vastcillin,vipicil,wyvital"					"NA"
-"CIX"	47472	"Ciclopirox"	"Antifungals/antimycotics"	"D01AE14,G01AX12,QD01AE14,QG01AX12"	"Antifungals for topical use"	"Other antifungals for topical use"	"cipx"	"NA"					"NA"
+"CIC"	19003	"Ciclacillin"	"Penicillins,Beta-lactams"	"NA"			"cyclac"	"bastcillin,calthor,ciclacilina,ciclacilline,ciclacillinum,ciclacillum,citosarin,cyclacillin,cyclapen,noblicil,orfilina,peamezin,syngacillin,ultracillin,vastcillin,vipicil,wyvital"					"NA"
+"CIX"	47472	"Ciclopirox"	"Antifungals"	"D01AE14,G01AX12,QD01AE14,QG01AX12"	"Antifungals for topical use"	"Other antifungals for topical use"	"cipx"	"NA"					"NA"
 "CIN"	2762	"Cinoxacin"	"Quinolones"	"J01MB06,QJ01MB06"	"Quinolone antibacterials"	"Other quinolones"	"cino,cinoxa,cnox"	"cinobac,cinobactin,cinoxacine,cinoxacino,cinoxacinum,clinoxacin,noxigram,uronorm"	1	"g"			"180-0,181-8,182-6,183-4,18905-0,55656-3"
-"CIP"	2764	"Ciprofloxacin"	"Fluoroquinolones"	"J01MA02,QJ01MA02,QS01AE03,QS02AA15,QS03AA07,S01AE03,S02AA15,S03AA07"	"Quinolone antibacterials"	"Fluoroquinolones"	"ci,cip,cipr,ciprof,cp"	"alcipro,bacquinor,baflox,belmacina,bernoflox,catex,cenin,ceprimax,cetraxal,ciflan,ciflosin,cifloxin,cilab,cilox,ciloxan,cipad,ciplus,ciprecu,ciprenit,ciprine,ciprinol,cipro,ciprobay,ciprocinal,ciprocinol,ciprodar,ciproflox,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprofur,ciprogis,ciproktan,ciprolin,ciprolon,cipromycin,cipronex,ciprooxacin,cipropol,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citeral,citopcin,cixan,corsacin,cunesin,cycin,cyprobay,cyproxan,disfabac,felixene,fimoflox,flociprin,floxacipron,flunas,globuce,inkamil,ipiflox,italnik,keefloxin,linhaliq,loxacid,loxan,lypro,megaflox,microgan,nixin,novidat,novoquin,ofitin,oftacilox,ophaflox,otiprio,phaproxin,piprol,plenolyt,probiox,proflaxin,proksi,proquin,proxacin,quinoflox,quinolid,quintor,quipro,rancif,renator,roflazin,roxytal,sepcen,septicide,septocipro,siprogut,sophixin,spitacin,strox,suiflox,superocin,supraflox,uritent,utiminx,velmonit,zumaflox"	1	"g"	0.8	"g"	"101500-7,14031-9,14032-7,14058-2,14059-0,184-2,185-9,186-7,187-5,18906-8,20377-8,23621-6,25180-1,25181-9,25188-4,25189-2,25248-6,34636-1,3484-3,42644-5,55194-5,7002-9"
-"CIM"		"Ciprofloxacin/metronidazole"	"Fluoroquinolones"	"J01RA10,QJ01RA10"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"CIO"		"Ciprofloxacin/ornidazole"	"Fluoroquinolones"	"J01RA12,QJ01RA12"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"CIT"		"Ciprofloxacin/tinidazole"	"Fluoroquinolones"	"J01RA11,QJ01RA11"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"CLR"	84029	"Clarithromycin"	"Macrolides/lincosamides"	"J01FA09,QJ01FA09"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"ch,cla,clar,claryt,clm,clr"	"abbotic,abboticine,astromen,biaxin,bicrolid,bristamycin,clacee,clacid,clacine,clambiotic,clarem,claribid,claricide,claridar,claripen,clarith,clarithromycine,clarithromycinum,claritromicina,clarosip,clathromycin,crixan,cyllid,cyllind,eratrex,esinol,fromilid,gallimycin,helas,heliclar,klabax,klacid,klaciped,klaricid,klarid,klarin,kofron,mabicrol,macladin,maclar,mavid,meberyt,pediamycin,qidmycin,veclam,wyamycin,zeclar"	0.5	"g"	1	"g"	"100048-8,16619-9,16620-7,188-3,189-1,18907-6,190-9,191-7,20375-2,23619-0,25190-0,25191-8,25192-6,25253-6,34638-7,43987-7,43990-1,43991-9,7003-7,80559-8,89485-7"
-"CLA1"	5280980	"Clavulanic acid"	"Other antibacterials"	"NA"			"NA"	"amonate,clavulanate,clavulanateacid,clavulansaeure,clavulansaure,clavulox,serdaxin"					"NA"
-"CLX"	60063	"Clinafloxacin"	"Fluoroquinolones"	"NA"			"clinaf"	"NA"					"32376-6,33284-1,35785-5,35786-3,7004-5"
-"CLI"	446598	"Clindamycin"	"Macrolides/lincosamides"	"D10AF01,G01AA10,J01FF01,QD10AF01,QG01AA10,QJ01FF01"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"cc,cd,cli,clin,clin32,clinda,cm,da"	"antirobe,chlolincocin,chlorlincocin,cleocin,clindamicina,clindamycine,clindamycinum,clinimycin,clinsol,clintabs,dalacine,klimicin,klindan,sobelin"	1.2	"g"	1.8	"g"	"16621-5,16622-3,18908-4,192-5,193-3,194-1,195-8,25249-4,3486-8,42720-3,55657-1,55658-9,55659-7,55660-5,61188-9,7005-2"
-"CLI-S"		"Clindamycin inducible screening test"	"Macrolides/lincosamides"	"NA"			"clin inducible,clinda inducible,clindamycin inducible"	"NA"					"NA"
+"CIP"	2764	"Ciprofloxacin"	"Fluoroquinolones,Quinolones"	"J01MA02,QJ01MA02,QS01AE03,QS02AA15,QS03AA07,S01AE03,S02AA15,S03AA07"	"Quinolone antibacterials"	"Fluoroquinolones"	"ci,cip,cipr,ciprof,cp"	"alcipro,bacquinor,baflox,belmacina,bernoflox,catex,cenin,ceprimax,cetraxal,ciflan,ciflosin,cifloxin,cilab,cilox,ciloxan,cipad,ciplus,ciprecu,ciprenit,ciprine,ciprinol,cipro,ciprobay,ciprocinal,ciprocinol,ciprodar,ciproflox,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprofur,ciprogis,ciproktan,ciprolin,ciprolon,cipromycin,cipronex,ciprooxacin,cipropol,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citeral,citopcin,cixan,corsacin,cunesin,cycin,cyprobay,cyproxan,disfabac,felixene,fimoflox,flociprin,floxacipron,flunas,globuce,inkamil,ipiflox,italnik,keefloxin,linhaliq,loxacid,loxan,lypro,megaflox,microgan,nixin,novidat,novoquin,ofitin,oftacilox,ophaflox,otiprio,phaproxin,piprol,plenolyt,probiox,proflaxin,proksi,proquin,proxacin,quinoflox,quinolid,quintor,quipro,rancif,renator,roflazin,roxytal,sepcen,septicide,septocipro,siprogut,sophixin,spitacin,strox,suiflox,superocin,supraflox,uritent,utiminx,velmonit,zumaflox"	1	"g"	0.8	"g"	"101500-7,14031-9,14032-7,14058-2,14059-0,184-2,185-9,186-7,187-5,18906-8,20377-8,23621-6,25180-1,25181-9,25188-4,25189-2,25248-6,34636-1,3484-3,42644-5,55194-5,7002-9"
+"CIM"		"Ciprofloxacin/metronidazole"	"Fluoroquinolones,Quinolones"	"J01RA10,QJ01RA10"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"CIO"		"Ciprofloxacin/ornidazole"	"Fluoroquinolones,Quinolones"	"J01RA12,QJ01RA12"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"CIT"		"Ciprofloxacin/tinidazole"	"Fluoroquinolones,Quinolones"	"J01RA11,QJ01RA11"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"CLR"	84029	"Clarithromycin"	"Macrolides"	"J01FA09,QJ01FA09"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"ch,cla,clar,claryt,clm,clr"	"abbotic,abboticine,astromen,biaxin,bicrolid,bristamycin,clacee,clacid,clacine,clambiotic,clarem,claribid,claricide,claridar,claripen,clarith,clarithromycine,clarithromycinum,claritromicina,clarosip,clathromycin,crixan,cyllid,cyllind,eratrex,esinol,fromilid,gallimycin,helas,heliclar,klabax,klacid,klaciped,klaricid,klarid,klarin,kofron,mabicrol,macladin,maclar,mavid,meberyt,pediamycin,qidmycin,veclam,wyamycin,zeclar"	0.5	"g"	1	"g"	"100048-8,16619-9,16620-7,188-3,189-1,18907-6,190-9,191-7,20375-2,23619-0,25190-0,25191-8,25192-6,25253-6,34638-7,43987-7,43990-1,43991-9,7003-7,80559-8,89485-7"
+"CLA1"	5280980	"Clavulanic acid"	"Other"	"NA"			"NA"	"amonate,clavulanate,clavulanateacid,clavulansaeure,clavulansaure,clavulox,serdaxin"					"NA"
+"CLX"	60063	"Clinafloxacin"	"Fluoroquinolones,Quinolones"	"NA"			"clinaf"	"NA"					"32376-6,33284-1,35785-5,35786-3,7004-5"
+"CLI"	446598	"Clindamycin"	"Lincosamides"	"D10AF01,G01AA10,J01FF01,QD10AF01,QG01AA10,QJ01FF01"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"cc,cd,cli,clin,clin32,clinda,cm,da"	"antirobe,chlolincocin,chlorlincocin,cleocin,clindamicina,clindamycine,clindamycinum,clinimycin,clinsol,clintabs,dalacine,klimicin,klindan,sobelin"	1.2	"g"	1.8	"g"	"16621-5,16622-3,18908-4,192-5,193-3,194-1,195-8,25249-4,3486-8,42720-3,55657-1,55658-9,55659-7,55660-5,61188-9,7005-2"
+"CLI-S"		"Clindamycin inducible screening test"	"Lincosamides,Macrolides"	"NA"			"clin inducible,clinda inducible,clindamycin inducible"	"NA"					"NA"
 "CLF"	2794	"Clofazimine"	"Antimycobacterials"	"J04BA01,QJ04BA01"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"clof,clofam"	"chlofazimine,clofazimina,clofaziminum,colfazimine,lampren,lamprene,phenazine,riminophenazine"	0.1	"g"			"16623-1,20376-0,23620-8,23627-3,43986-9,43988-5,43989-3,55661-3,55662-1,96108-6"
-"CLF1"	2799	"Clofoctol"	"Other antibacterials"	"J01XX03,QJ01XX03"	"Other antibacterials"	"Other antibacterials"	"NA"	"clofoctolo,clofoctolum,gramplus,octofene,phenol"					"NA"
-"CLM"	71807	"Clometocillin"	"Beta-lactams/penicillins"	"J01CE07,QJ01CE07"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"chlomethocillin,clometacillin,clomethacillin,clomethocillin,clometocilina,clometocilline,clometocillinsalt,clometocillinum,penicilline,rixapen"	1	"g"			"NA"
+"CLF1"	2799	"Clofoctol"	"Other"	"J01XX03,QJ01XX03"	"Other antibacterials"	"Other antibacterials"	"NA"	"clofoctolo,clofoctolum,gramplus,octofene,phenol"					"NA"
+"CLM"	71807	"Clometocillin"	"Penicillins,Beta-lactams"	"J01CE07,QJ01CE07"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"chlomethocillin,clometacillin,clomethacillin,clomethocillin,clometocilina,clometocilline,clometocillinsalt,clometocillinum,penicilline,rixapen"	1	"g"			"NA"
 "CLM1"	54680675	"Clomocycline"	"Tetracyclines"	"J01AA11,QJ01AA11"	"Tetracyclines"	"Tetracyclines"	"NA"	"clomociclina,clomocyclinum,megaclor"	1	"g"			"NA"
-"CTR"	2812	"Clotrimazole"	"Antifungals/antimycotics"	"A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90"			"clot"	"alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole"					"10653-4,10654-2,18909-2,54177-1,55663-9"
-"CLO"	6098	"Cloxacillin"	"Beta-lactams/penicillins"	"J01CF02,QJ01CF02,QJ51CF02,QS01AA90"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox,cloxac"	"ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,tegopen"	2	"g"	2	"g"	"16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7"
+"CTR"	2812	"Clotrimazole"	"Antifungals"	"A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90"			"clot"	"alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole"					"10653-4,10654-2,18909-2,54177-1,55663-9"
+"CLO"	6098	"Cloxacillin"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"J01CF02,QJ01CF02,QJ51CF02,QS01AA90"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox,cloxac"	"ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,tegopen"	2	"g"	2	"g"	"16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7"
 "COL"	5311054	"Colistin"	"Polymyxins"	"A07AA10,J01XB01,QA07AA10,QJ01XB01,QJ51XB01"	"Other antibacterials"	"Polymyxins"	"cl,coli,colist,cs,cst,ct"	"colimycin,colisticin,colisticina,colistina,colistine,colistinum,colobreathe,colomycin,kangdisu,kolimitsin,kolimycin,promixin,sogecoli,totazina"	9	"MU"	9	"MU"	"16645-4,18912-6,204-8,205-5,206-3,207-1,29493-4,33333-6"
-"COP"		"Colistin/polysorbate"	"Other antibacterials"	"NA"			"NA"	"NA"					"NA"
+"COP"		"Colistin/polysorbate"	"Other"	"NA"			"NA"	"NA"					"NA"
 "CYC"	6234	"Cycloserine"	"Oxazolidinones"	"J04AB01,QJ04AB01"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"cycl,cyclos"	"cicloserina,closina,cyclorin,cycloserin,cycloserinum,farmiserina,levcicloserina,levcycloserine,levcycloserinum,micoserina,miroserina,miroseryn,novoserin,oxamicina,oxamycin,seromycin,tebemicina,wasserina"	0.75	"g"			"16702-3,18914-2,212-1,213-9,214-7,215-4,23608-3,25207-2,25208-0,25209-8,25251-0,3519-6,55667-0"
-"DAL"	23724878	"Dalbavancin"	"Glycopeptides"	"J01XA04,QJ01XA04"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb,dalbav"	"dalbavancina,dalvance,xydalba,zeven"			1.5	"g"	"41688-3,41689-1,41690-9,41734-5"
-"DAN"	71335	"Danofloxacin"	"Fluoroquinolones"	"QJ01MA92"			"danofl"	"advocin,danofloxacine,danofloxacino,danofloxacinum"					"73601-7,73623-1,73646-2"
-"DPS"	2955	"Dapsone"	"Other antibacterials"	"D10AX05,J04BA02,QD10AX05,QJ04BA02"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"NA"	"aczone,atrisone,avlosulfon,avlosulfone,avlosulphone,benzenamide,benzenamine,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsonum,daspone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dumitone,eporal,medapsol,novophone,servidapson,sulfadione,sulfona,sulfonyldianiline,sulphadione,sulphonyldianiline,tarimyl,udolac,undolac"	50	"mg"			"51698-9,9747-7"
-"DAP"	16134395	"Daptomycin"	"Other antibacterials"	"J01XX09,QJ01XX09"	"Other antibacterials"	"Other antibacterials"	"dap,dapt,dapt25,dapt50,daptom"	"cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum,deptomycin"			0.28	"g"	"35787-1,35788-9,35789-7,41691-7"
-"DFX"	487101	"Delafloxacin"	"Fluoroquinolones"	"J01MA23,QJ01MA23"			"NA"	"baxdela,delafloxacinum,quofenix"	0.9	"g"	0.6	"g"	"88885-9,90447-4,93790-4"
+"DAL"	23724878	"Dalbavancin"	"Lipoglycopeptides,Glycopeptides"	"J01XA04,QJ01XA04"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb,dalbav"	"dalbavancina,dalvance,xydalba,zeven"			1.5	"g"	"41688-3,41689-1,41690-9,41734-5"
+"DAN"	71335	"Danofloxacin"	"Fluoroquinolones,Quinolones"	"QJ01MA92"			"danofl"	"advocin,danofloxacine,danofloxacino,danofloxacinum"					"73601-7,73623-1,73646-2"
+"DPS"	2955	"Dapsone"	"Other"	"D10AX05,J04BA02,QD10AX05,QJ04BA02"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"dao"	"aczone,atrisone,avlosulfon,avlosulfone,avlosulphone,benzenamide,benzenamine,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsonum,daspone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dumitone,eporal,medapsol,novophone,servidapson,sulfadione,sulfona,sulfonyldianiline,sulphadione,sulphonyldianiline,tarimyl,udolac,undolac"	50	"mg"			"51698-9,9747-7"
+"DAP"	16134395	"Daptomycin"	"Other"	"J01XX09,QJ01XX09"	"Other antibacterials"	"Other antibacterials"	"dap,dapt,dapt25,dapt50,daptom"	"cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum,deptomycin"			0.28	"g"	"35787-1,35788-9,35789-7,41691-7"
+"DFX"	487101	"Delafloxacin"	"Fluoroquinolones,Quinolones"	"J01MA23,QJ01MA23"			"NA"	"baxdela,delafloxacinum,quofenix"	0.9	"g"	0.6	"g"	"88885-9,90447-4,93790-4"
 "DLM"	6480466	"Delamanid"	"Antimycobacterials"	"J04AK06,QJ04AK06"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"dela"	"deltyba"	0.2	"g"			"93851-4,96109-4"
 "DEM"	54680690	"Demeclocycline"	"Tetracyclines"	"D06AA01,J01AA01,QD06AA01,QJ01AA01"	"Tetracyclines"	"Tetracyclines"	"demecy"	"demeclociclina,demeclocyclinum"	0.6	"g"			"10982-7,18915-9,216-2,217-0,218-8,219-6,29494-2,7006-0"
 "DKB"	470999	"Dibekacin"	"Aminoglycosides"	"J01GB09,QJ01GB09,QS01AA29,S01AA29"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"dibeka"	"debecacin,dibekacina,dibekacine,dibekacinum,kappati,panamicin"			0.14	"g"	"55669-6,55670-4,55671-2,55672-0"
-"DIC"	18381	"Dicloxacillin"	"Beta-lactams/penicillins"	"J01CF01,QJ01CF01,QJ51CF01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"dicl,diclox"	"dichloroxacillin,diclossacillina,dicloxaciclin,dicloxacilin,dicloxacilina,dicloxacillina,dicloxacilline,dicloxacillinum,dicloxacycline,maclicine"	2	"g"	2	"g"	"10984-3,16769-2,18916-7,220-4,221-2,222-0,223-8,25252-8,32380-8,55668-8"
-"DIF"	56206	"Difloxacin"	"Fluoroquinolones"	"QJ01MA94"			"diflox"	"dicural,difloxacine,pulsaflox"					"35790-5,35791-3,35792-1"
-"DIR"	6473883	"Dirithromycin"	"Macrolides/lincosamides"	"J01FA13,QJ01FA13"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"dirith"	"dirithromycine,dirithromycinum,diritromicina,divitross,dynabac,noriclan,valodin"	0.5	"g"			"35793-9,35794-7,35795-4,7007-8"
-"DOR"	73303	"Doripenem"	"Carbapenems"	"J01DH04,QJ01DH04"	"Other beta-lactam antibacterials"	"Carbapenems"	"dori,doripe"	"doribax,dripenem,finibax"			1.5	"g"	"56031-8,58711-3,60535-2,72893-1"
+"DIC"	18381	"Dicloxacillin"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"J01CF01,QJ01CF01,QJ51CF01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"dicl,diclox"	"dichloroxacillin,diclossacillina,dicloxaciclin,dicloxacilin,dicloxacilina,dicloxacillina,dicloxacilline,dicloxacillinum,dicloxacycline,maclicine"	2	"g"	2	"g"	"10984-3,16769-2,18916-7,220-4,221-2,222-0,223-8,25252-8,32380-8,55668-8"
+"DIF"	56206	"Difloxacin"	"Fluoroquinolones,Quinolones"	"QJ01MA94"			"diflox"	"dicural,difloxacine,pulsaflox"					"35790-5,35791-3,35792-1"
+"DIR"	6473883	"Dirithromycin"	"Macrolides"	"J01FA13,QJ01FA13"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"dirith"	"dirithromycine,dirithromycinum,diritromicina,divitross,dynabac,noriclan,valodin"	0.5	"g"			"35793-9,35794-7,35795-4,7007-8"
+"DOR"	73303	"Doripenem"	"Carbapenems,Beta-lactams"	"J01DH04,QJ01DH04"	"Other beta-lactam antibacterials"	"Carbapenems"	"dori,doripe"	"doribax,dripenem,finibax"			1.5	"g"	"56031-8,58711-3,60535-2,72893-1"
 "DOX"	54671203	"Doxycycline"	"Tetracyclines"	"A01AB22,J01AA02,QA01AB22,QJ01AA02"	"Tetracyclines"	"Tetracyclines"	"dox,doxy,doxycy"	"abbocin,alamycin,aquacycline,biosolvomycin,biotet,bisolvomycin,chrysocin,dalimycin,dalinmycin,deoxymykoin,dossiciclina,doxiciclina,doxirobe,doxitard,doxivetin,doxycen,doxychel,doxycin,doxycyclin,doxycyclinum,doxylin,doxysol,doxytetracycline,elinton,engemycin,hydrocyclin,imperacin,intaloxin,investin,jenacyclin,liquachel,liviatin,macodyn,mepatar,microdox,mondoxyne,monodox,morgidox,ocudox,okebo,oracea,otetryn,oxacycline,oxamycen,oxatet,oxlopar,oxybiocycline,oxydon,oxyject,oxymykoin,oxysteclin,oxytet,oxytetral,oxytetrin,oxytracyl,oxyvet,stecsolin,supracyclin,terraject,terramycin,toxinal,unimycin,vendarcin,vibramycin,vibramycine,vivox,zenavod"	0.1	"g"	0.1	"g"	"10986-8,18917-5,20379-4,21250-6,224-6,225-3,226-1,227-9,23623-2,25223-9,26902-7,7008-6"
-"ECO"	3198	"Econazole"	"Antifungals/antimycotics"	"D01AC03,G01AF05,QD01AC03,QG01AF05"	"Antifungals for topical use"	"Imidazole and triazole derivatives"	"econ"	"bromazil,chloramizol,clinafarm,deccosil,deccozil,econazolum,ecostatin,ekonazole,enilconazol,enilconazole,eniloconazol,fecundal,florasan,freshgard,freshguard,fungaflor,fungazil,imaverol,imaversol,imazalil,magnate,spectazole"					"25595-0,25637-0,54178-9,55673-8"
+"ECO"	3198	"Econazole"	"Antifungals"	"D01AC03,G01AF05,QD01AC03,QG01AF05"	"Antifungals for topical use"	"Imidazole and triazole derivatives"	"econ"	"bromazil,chloramizol,clinafarm,deccosil,deccozil,econazolum,ecostatin,ekonazole,enilconazol,enilconazole,eniloconazol,fecundal,florasan,freshgard,freshguard,fungaflor,fungazil,imaverol,imaversol,imazalil,magnate,spectazole"					"25595-0,25637-0,54178-9,55673-8"
 "EFF"		"Efflux"	"Other"	"NA"			"effflux pump"	"NA"					"NA"
-"ENX"	3229	"Enoxacin"	"Fluoroquinolones"	"J01MA04,QJ01MA04"	"Quinolone antibacterials"	"Fluoroquinolones"	"enox,enoxa"	"abenox,almitil,bactidan,bactidron,comprecin,enofloxacine,enoksetin,enoram,enoxacina,enoxacine,enoxacino,enoxacinum,enoxen,enoxin,enoxor,flumark,penetrex"	0.8	"g"			"16816-1,18918-3,228-7,229-5,230-3,231-1,3590-7,41692-5"
-"ENR"	71188	"Enrofloxacin"	"Fluoroquinolones"	"QJ01MA90"			"enrofl"	"baytril,enroflox,enrofloxacine,enrofloxacino,enrofloxacinum,enroquin,enrosite,enroxil,quellaxcin,tenotryl,zobuxa"					"23712-3,35796-2,35797-0,35798-8"
+"ENX"	3229	"Enoxacin"	"Fluoroquinolones,Quinolones"	"J01MA04,QJ01MA04"	"Quinolone antibacterials"	"Fluoroquinolones"	"enox,enoxa"	"abenox,almitil,bactidan,bactidron,comprecin,enofloxacine,enoksetin,enoram,enoxacina,enoxacine,enoxacino,enoxacinum,enoxen,enoxin,enoxor,flumark,penetrex"	0.8	"g"			"16816-1,18918-3,228-7,229-5,230-3,231-1,3590-7,41692-5"
+"ENR"	71188	"Enrofloxacin"	"Fluoroquinolones,Quinolones"	"QJ01MA90"			"enrofl"	"baytril,enroflox,enrofloxacine,enrofloxacino,enrofloxacinum,enroquin,enrosite,enroxil,quellaxcin,tenotryl,zobuxa"					"23712-3,35796-2,35797-0,35798-8"
 "ENV"	135565326	"Enviomycin"	"Antimycobacterials"	"J04AB06,QJ04AB06"			"tuberactinomycin"	"enviomicina,enviomycina,enviomycine,enviomycinum,tuberactin"			1	"g"	"NA"
-"EPE"		"Eperozolid"	"Other antibacterials"	"NA"			"NA"	"NA"					"NA"
-"EPC"	71392	"Epicillin"	"Beta-lactams/penicillins"	"J01CA07,QJ01CA07"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"dexacillin,dihydroampicillin,epicilina,epicilline,epicillinum,spectacillin"	2	"g"	2	"g"	"NA"
-"EPP"	68916	"Epiroprim"	"Other antibacterials"	"NA"			"NA"	"epiroprima,epiroprime,epiroprimum"					"NA"
+"EPE"		"Eperozolid"	"Other"	"NA"			"NA"	"NA"					"NA"
+"EPC"	71392	"Epicillin"	"Penicillins,Beta-lactams"	"J01CA07,QJ01CA07"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"dexacillin,dihydroampicillin,epicilina,epicilline,epicillinum,spectacillin"	2	"g"	2	"g"	"NA"
+"EPP"	68916	"Epiroprim"	"Other"	"NA"			"NA"	"epiroprima,epiroprime,epiroprimum"					"NA"
 "ERV"	54726192	"Eravacycline"	"Tetracyclines"	"J01AA13,QJ01AA13"	"Tetracyclines"	"Tetracyclines"	"erav"	"xerava"			0.14	"g"	"100049-6,85423-2,93767-2"
-"ETP"	150610	"Ertapenem"	"Carbapenems"	"J01DH03,QJ01DH03"	"Other beta-lactam antibacterials"	"Carbapenems"	"erta,ertape,etp"	"ertapenemsalt,invanz"			1	"g"	"101486-9,35799-6,35800-2,35801-0,35802-8"
-"ERY"	12560	"Erythromycin"	"Macrolides/lincosamides"	"D10AF02,J01FA01,QD10AF02,QJ01FA01,QJ51FA01,QS01AA17,S01AA17"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"e,em,ery,ery32,eryt,eryth"	"abboticin,abomacetin,acneryne,acnesol,aknemycin,aknin,benzamycin,derimer,deripil,dotycin,dumotrycin,emgel,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,erycen,erycette,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erysafe,erytab,erythro,erythroderm,erythrogran,erythroguent,erythromast,erythromid,erythromycine,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,inderm,latotryd,lederpax,mephamycin,mercina,oftamolets,pantoderm,pantodrin,pantomicina,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,sansac,spotex,staticin,stiemicyn,stiemycin,tiprocin,torlamicina,wemid"	2	"g"	1	"g"	"100050-4,11576-6,12298-6,16829-4,16830-2,18919-1,18920-9,20380-2,232-9,233-7,234-5,235-2,236-0,23633-1,237-8,238-6,239-4,25224-7,25275-9,3597-2,7009-4"
-"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02,QJ04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"etha,ethamb"	"aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,purderal,servambutol,tibutol"	1.2	"g"	1.2	"g"	"100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
+"ETP"	150610	"Ertapenem"	"Carbapenems,Beta-lactams"	"J01DH03,QJ01DH03"	"Other beta-lactam antibacterials"	"Carbapenems"	"erta,ertape,etp"	"ertapenemsalt,invanz"			1	"g"	"101486-9,35799-6,35800-2,35801-0,35802-8"
+"ERY"	12560	"Erythromycin"	"Macrolides"	"D10AF02,J01FA01,QD10AF02,QJ01FA01,QJ51FA01,QS01AA17,S01AA17"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"e,em,ery,ery32,eryt,eryth"	"abboticin,abomacetin,acneryne,acnesol,aknemycin,aknin,benzamycin,derimer,deripil,dotycin,dumotrycin,emgel,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,erycen,erycette,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erysafe,erytab,erythro,erythroderm,erythrogran,erythroguent,erythromast,erythromid,erythromycine,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,inderm,latotryd,lederpax,mephamycin,mercina,oftamolets,pantoderm,pantodrin,pantomicina,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,sansac,spotex,staticin,stiemicyn,stiemycin,tiprocin,torlamicina,wemid"	2	"g"	1	"g"	"100050-4,11576-6,12298-6,16829-4,16830-2,18919-1,18920-9,20380-2,232-9,233-7,234-5,235-2,236-0,23633-1,237-8,238-6,239-4,25224-7,25275-9,3597-2,7009-4"
+"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02,QJ04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"emb,etha,ethamb"	"aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,purderal,servambutol,tibutol"	1.2	"g"	1.2	"g"	"100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
 "ETI"	456476	"Ethambutol/isoniazid"	"Antimycobacterials"	"J04AM03,QJ04AM03"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
 "ETI1"	2761171	"Ethionamide"	"Antimycobacterials"	"J04AD03,QJ04AD03"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi,ethion"	"aethionamidum,aetina,aetiva,amidazin,amidazine,atina,ethimide,ethina,ethinamide,ethionamidum,ethioniamide,ethylisothiamide,ethyonomide,etimid,etiocidan,etionamid,etionamida,etionamide,etioniamid,etionid,etionizin,etionizina,etionizine,fatoliamid,iridocin,iridozin,isothin,isotiamida,itiocide,nicotion,nisotin,nizotin,rigenicid,sertinon,teberus,thianid,thianide,thioamide,thiodine,thiomid,thioniden,tianid,tiomid,trecator,trekator,trescatyl,trescazide,tubenamide,tubermin,tuberoid,tuberoson"	0.75	"g"			"16099-4,16845-0,18922-5,20382-8,23617-4,25183-5,25196-7,25198-3,25231-2,41693-3,42647-8,42648-6,7011-0,96110-2"
-"ETO"	6034	"Ethopabate"	"Other antibacterials"	"QP51AX17"			"NA"	"ethopabat"					"NA"
-"EXE"		"Exebacase"		"NA"			"NA"	"NA"					"NA"
-"FAR"	65894	"Faropenem"	"Other antibacterials"	"J01DI03,QJ01DI03"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	"farope"	"farom,faropenemhydrate,faropenemsalt,fropenem,fropenum,furopenem"	0.75	"g"			"73600-9,73622-3,73645-4"
-"FDX"	10034073	"Fidaxomicin"	"Other antibacterials"	"A07AA12,QA07AA12"			"NA"	"dificid,dificlir,difimicin,fidaxomicina,lipiarmicin,lipiarmycin,lipiarrmycin"	0.4	"g"			"73599-3,73621-5,73644-7"
-"FIN"	11567473	"Finafloxacin"	"Fluoroquinolones"	"NA"			"NA"	"xtoro"					"73598-5,73620-7,73643-9"
-"FLA"	46783781	"Flavomycin"	"Other antibacterials"	"NA"			"flavom"	"bambermicina,bambermycine,bambermycinum,flavofosfolipol,flavophospholipol,gainpro,menomycin"					"NA"
-"FLE"	3357	"Fleroxacin"	"Fluoroquinolones"	"J01MA08,QJ01MA08"	"Quinolone antibacterials"	"Fluoroquinolones"	"fler,flerox"	"fleroxacine,fleroxacino,fleroxacinum,fleroxicin,megalocin,megalone,megalosin,quinodis"	0.4	"g"	0.4	"g"	"25411-0,32372-5,35806-9,7012-8"
-"FLO"	65864	"Flomoxef"	"Other antibacterials"	"J01DC14,QJ01DC14"			"flomox"	"flomoxefo,flomoxefsalt,flomoxefum,flumarin"			2	"g"	"100052-0,53822-3"
+"ETO"	6034	"Ethopabate"	"Other"	"QP51AX17"			"NA"	"ethopabat"					"NA"
+"EXE"		"Exebacase"	"Other"	"NA"			"NA"	"NA"					"NA"
+"FAR"	65894	"Faropenem"	"Other"	"J01DI03,QJ01DI03"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	"farope"	"farom,faropenemhydrate,faropenemsalt,fropenem,fropenum,furopenem"	0.75	"g"			"73600-9,73622-3,73645-4"
+"FDX"	10034073	"Fidaxomicin"	"Other"	"A07AA12,QA07AA12"			"NA"	"dificid,dificlir,difimicin,fidaxomicina,lipiarmicin,lipiarmycin,lipiarrmycin"	0.4	"g"			"73599-3,73621-5,73644-7"
+"FIN"	11567473	"Finafloxacin"	"Fluoroquinolones,Quinolones"	"NA"			"NA"	"xtoro"					"73598-5,73620-7,73643-9"
+"FLA"	46783781	"Flavomycin"	"Other"	"NA"			"flavom"	"bambermicina,bambermycine,bambermycinum,flavofosfolipol,flavophospholipol,gainpro,menomycin"					"NA"
+"FLE"	3357	"Fleroxacin"	"Fluoroquinolones,Quinolones"	"J01MA08,QJ01MA08"	"Quinolone antibacterials"	"Fluoroquinolones"	"fler,flerox"	"fleroxacine,fleroxacino,fleroxacinum,fleroxicin,megalocin,megalone,megalosin,quinodis"	0.4	"g"	0.4	"g"	"25411-0,32372-5,35806-9,7012-8"
+"FLO"	65864	"Flomoxef"	"Other"	"J01DC14,QJ01DC14"			"flomox"	"flomoxefo,flomoxefsalt,flomoxefum,flumarin"			2	"g"	"100052-0,53822-3"
 "FLR"	114811	"Florfenicol"	"Phenicols"	"QJ01BA90,QJ51BA90"			"florfe"	"aquafen,descocin,dexawin,efnicol,fricol,hyrazin,loncor,macphenicol,masatirin,neomyson,norfenicol,nuflor,racephenicol,rincrol,thiamcol,urfamicina,urophenyl"					"23740-4,35807-7,35808-5,87599-7"
-"FLC"	21319	"Flucloxacillin"	"Beta-lactams/penicillins"	"J01CF05,QJ01CF05,QJ51CF05"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox,fluclo,flux"	"bactopen,cloxacap,cloxacillinhydrate,cloxypen,floxacillin,floxacillinanhydrous,floxapen,floxapensalt,fluclomix,flucloxacilina,flucloxacilline,flucloxacillinum,flucloxin,fluorochloroxacillin,galfloxin,latocillin,orbeninhydrate,rimaflox,staphobristol,zoxin"	2	"g"	2	"g"	"NA"
-"FLU"	3365	"Fluconazole"	"Antifungals/antimycotics"	"D01AC15,J02AC01,QD01AC15,QJ02AC01"	"Antimycotics for systemic use"	"Triazole derivatives"	"fluc,flucon,fluz,flz"	"alflucoz,alkanazole,baten,biocanol,biozole,biozolene,canzol,cryptal,diflazon,diflucan,dimycon,elazor,flucazol,fluconazoli,fluconazolum,flucoral,flucostat,flukezol,flunazol,flunizol,fluzon,forcan,fuconal,fungata,loitin,mutum,oxifugol,pritenzol,syscan,trican,triconal,triflucan,zemyc,zoltec,zonal"	0.2	"g"	0.2	"g"	"10987-6,16870-8,18924-1,248-5,249-3,250-1,251-9,25255-1,7013-6,80530-9"
-"FCT"	3366	"Flucytosine"	"Antifungals/antimycotics"	"D01AE21,J02AX01,QD01AE21,QJ02AX01"	"Antifungals for topical use"	"Other antifungals for topical use"	"5flc,fcu,flucyt,fluo,fluy"	"alcobon,ancoban,ancobon,ancotil,ancotyl,flourocytosine,flucitosina,flucytosin,flucytosinum,flucytosone,fluocytosine,fluorcytosine,fluorocytosine"	10	"g"	10	"g"	"NA"
+"FLC"	21319	"Flucloxacillin"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"J01CF05,QJ01CF05,QJ51CF05"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox,fluclo,flux"	"bactopen,cloxacap,cloxacillinhydrate,cloxypen,floxacillin,floxacillinanhydrous,floxapen,floxapensalt,fluclomix,flucloxacilina,flucloxacilline,flucloxacillinum,flucloxin,fluorochloroxacillin,galfloxin,latocillin,orbeninhydrate,rimaflox,staphobristol,zoxin"	2	"g"	2	"g"	"NA"
+"FLU"	3365	"Fluconazole"	"Antifungals"	"D01AC15,J02AC01,QD01AC15,QJ02AC01"	"Antimycotics for systemic use"	"Triazole derivatives"	"fluc,flucon,fluz,flz"	"alflucoz,alkanazole,baten,biocanol,biozole,biozolene,canzol,cryptal,diflazon,diflucan,dimycon,elazor,flucazol,fluconazoli,fluconazolum,flucoral,flucostat,flukezol,flunazol,flunizol,fluzon,forcan,fuconal,fungata,loitin,mutum,oxifugol,pritenzol,syscan,trican,triconal,triflucan,zemyc,zoltec,zonal"	0.2	"g"	0.2	"g"	"10987-6,16870-8,18924-1,248-5,249-3,250-1,251-9,25255-1,7013-6,80530-9"
+"FCT"	3366	"Flucytosine"	"Antifungals"	"D01AE21,J02AX01,QD01AE21,QJ02AX01"	"Antifungals for topical use"	"Other antifungals for topical use"	"5flc,fcu,flucyt,fluo,fluy"	"alcobon,ancoban,ancobon,ancotil,ancotyl,flourocytosine,flucitosina,flucytosin,flucytosinum,flucytosone,fluocytosine,fluorcytosine,fluorocytosine"	10	"g"	10	"g"	"NA"
 "FLM"	3374	"Flumequine"	"Quinolones"	"J01MB07,QJ01MB07"	"Quinolone antibacterials"	"Other quinolones"	"flumeq"	"apurone,fantacin,flumequina,flumequino,flumequinum,flumigal,flumiquil,flumisol,flumix,imequyl"	1.2	"g"			"55675-3,55676-1,55677-9,55678-7"
-"FLR1"	71260	"Flurithromycin"	"Macrolides/lincosamides"	"J01FA14,QJ01FA14"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"NA"	"abbot,beritromicina,berythromycin,berythromycine,berythromycinum,flurithromycine,flurithromycinum,fluritromicina,fluritromycinum,flurizic,mizar"	0.75	"g"			"NA"
-"FFL"	214356	"Fosfluconazole"	"Antifungals/antimycotics"	"NA"			"NA"	"fosfluconazol,procif,prodif"					"NA"
-"FOS"	446987	"Fosfomycin"	"Other antibacterials"	"J01XX01,QJ01XX01,QS02AA17,S02AA17"	"Other antibacterials"	"Other antibacterials"	"ff,fm,fo,fof,fos,fosf,fosfom,fosmyc"	"fosfocina,fosfomicin,fosfomicina,fosfomycine,fosfomycinum,fosfonomycin,infectophos,phosphonemycin,phosphonomycin,veramina"	3	"g"	8	"g"	"25596-8,25653-7,35809-3,35810-1"
-"FMD"	572	"Fosmidomycin"	"Other antibacterials"	"NA"			"NA"	"fosmidomicina,fosmidomycina,fosmidomycine,fosmidomycinsalt,fosmidomycinum"					"NA"
+"FLR1"	71260	"Flurithromycin"	"Macrolides"	"J01FA14,QJ01FA14"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"NA"	"abbot,beritromicina,berythromycin,berythromycine,berythromycinum,flurithromycine,flurithromycinum,fluritromicina,fluritromycinum,flurizic,mizar"	0.75	"g"			"NA"
+"FFL"	214356	"Fosfluconazole"	"Antifungals"	"NA"			"NA"	"fosfluconazol,procif,prodif"					"NA"
+"FOS"	446987	"Fosfomycin"	"Phosphonics"	"J01XX01,QJ01XX01,QS02AA17,S02AA17"	"Other antibacterials"	"Other antibacterials"	"ff,fm,fo,fof,fos,fosf,fosfom,fosmyc"	"fosfocina,fosfomicin,fosfomicina,fosfomycine,fosfomycinum,fosfonomycin,infectophos,phosphonemycin,phosphonomycin,veramina"	3	"g"	8	"g"	"25596-8,25653-7,35809-3,35810-1"
+"FMD"	572	"Fosmidomycin"	"Other"	"NA"			"NA"	"fosmidomicina,fosmidomycina,fosmidomycine,fosmidomycinsalt,fosmidomycinum"					"NA"
 "FRM"	8378	"Framycetin"	"Aminoglycosides"	"D09AA01,QD09AA01,QJ01GB91,QR01AX08,QS01AA07,R01AX08,S01AA07"			"fram,framyc"	"actilin,actiline,antibiotique,bycomycin,enterfram,fradiomycin,fradiomycinum,framicetina,framidal,framycetine,framycetinum,framycin,framygen,francetin,jernadex,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycine,neomycinum,nivemycin,soframycin,soframycine"					"18926-6,257-6,258-4,259-2,260-0,55679-5"
-"FUR"	6870646	"Furazidin"	"Other antibacterials"	"J01XE03,QJ01XE03"	"Other antibacterials"	"Nitrofuran derivatives"	"NA"	"akritoin,furagin,furaginum,furamag,furazidine,hydantoin"	0.3	"g"			"NA"
-"FRZ"	5323714	"Furazolidone"	"Other antibacterials"	"G01AX06,QG01AX06,QJ01XE90"			"furazo"	"bifuron,corizium,coryzium,diafuron,enterotoxon,furall,furanzolidone,furaxon,furaxone,furazolidine,furazolidon,furazolidona,furazolidonum,furazolum,furidon,furmethoxadone,furovag,furoxal,furoxane,furoxon,furoxone,furozolidine,giardil,giarlam,medaron,neftin,nicolen,nifulidone,nifuran,nifurazolidone,nifurazolidonum,nitrofuradoxon,nitrofurazolidone,nitrofurazolidonum,nitrofuroxon,optazol,ortazol,puradin,roptazol,sclaventerol,tikofuran,topazone,trichofuron,tricofuron,tricoron,trifurox,viofuragyn"					"69574-2,87794-4"
-"FUS"	3000226	"Fusidic acid"	"Other antibacterials"	"D06AX01,D09AA02,J01XC01,QD06AX01,QD09AA02,QJ01XC01,QS01AA13,S01AA13"	"Other antibacterials"	"Steroid antibacterials"	"fa,fusaci,fusi"	"flucidin,fucidate,fucidina,fucidine,fucithalmic,fusidate,fusidicacid,fusidin,fusidine,taksta"	1.5	"g"	1.5	"g"	"NA"
-"GAM"	59364992	"Gamithromycin"	"Macrolides/lincosamides"	"QJ01FA95"			"NA"	"zactran"					"100054-6,88376-9,88378-5"
-"GRN"	124093	"Garenoxacin"	"Fluoroquinolones"	"J01MA19,QJ01MA19"			"gareno"	"ganefloxacin,garenfloxacin"	0.4	"g"			"35811-9,35812-7,35813-5"
-"GAT"	5379	"Gatifloxacin"	"Fluoroquinolones"	"J01MA16,QJ01MA16,QS01AE06,S01AE06"	"Quinolone antibacterials"	"Fluoroquinolones"	"gati,gatifl"	"acorafloxacin,avarofloxacin,balofloxacin,balofox,bazucin,bilimin,bonoq,gaity,gatiflo,gatifloxacine,gatifloxcin,gatilox,gatiquin,gatispan,kinome,tequin,tymer,zymar,zymaxid,zymer"	0.4	"g"	0.4	"g"	"31036-7,31038-3,31040-9,31042-5,41494-6"
-"GEM"	9571107	"Gemifloxacin"	"Fluoroquinolones"	"J01MA15,QJ01MA15"	"Quinolone antibacterials"	"Fluoroquinolones"	"gemifl"	"factiv,gemifioxacin,gemifloxacine,gemifloxacino,gemifloxacinum"	0.32	"g"	0.2	"g"	"35814-3,35815-0,35816-8,41697-4"
+"FUR"	6870646	"Furazidin"	"Nitrofurans"	"J01XE03,QJ01XE03"	"Other antibacterials"	"Nitrofuran derivatives"	"NA"	"akritoin,furagin,furaginum,furamag,furazidine,hydantoin"	0.3	"g"			"NA"
+"FRZ"	5323714	"Furazolidone"	"Nitrofurans"	"G01AX06,QG01AX06,QJ01XE90"			"furazo"	"bifuron,corizium,coryzium,diafuron,enterotoxon,furall,furanzolidone,furaxon,furaxone,furazolidine,furazolidon,furazolidona,furazolidonum,furazolum,furidon,furmethoxadone,furovag,furoxal,furoxane,furoxon,furoxone,furozolidine,giardil,giarlam,medaron,neftin,nicolen,nifulidone,nifuran,nifurazolidone,nifurazolidonum,nitrofuradoxon,nitrofurazolidone,nitrofurazolidonum,nitrofuroxon,optazol,ortazol,puradin,roptazol,sclaventerol,tikofuran,topazone,trichofuron,tricofuron,tricoron,trifurox,viofuragyn"					"69574-2,87794-4"
+"FUS"	3000226	"Fusidic acid"	"Other"	"D06AX01,D09AA02,J01XC01,QD06AX01,QD09AA02,QJ01XC01,QS01AA13,S01AA13"	"Other antibacterials"	"Steroid antibacterials"	"fa,fusaci,fusi"	"flucidin,fucidate,fucidina,fucidine,fucithalmic,fusidate,fusidicacid,fusidin,fusidine,taksta"	1.5	"g"	1.5	"g"	"NA"
+"GAM"	59364992	"Gamithromycin"	"Macrolides"	"QJ01FA95"			"NA"	"zactran"					"100054-6,88376-9,88378-5"
+"GRN"	124093	"Garenoxacin"	"Fluoroquinolones,Quinolones"	"J01MA19,QJ01MA19"			"gareno"	"ganefloxacin,garenfloxacin"	0.4	"g"			"35811-9,35812-7,35813-5"
+"GAT"	5379	"Gatifloxacin"	"Fluoroquinolones,Quinolones"	"J01MA16,QJ01MA16,QS01AE06,S01AE06"	"Quinolone antibacterials"	"Fluoroquinolones"	"gati,gatifl"	"acorafloxacin,avarofloxacin,balofloxacin,balofox,bazucin,bilimin,bonoq,gaity,gatiflo,gatifloxacine,gatifloxcin,gatilox,gatiquin,gatispan,kinome,tequin,tymer,zymar,zymaxid,zymer"	0.4	"g"	0.4	"g"	"31036-7,31038-3,31040-9,31042-5,41494-6"
+"GEM"	9571107	"Gemifloxacin"	"Fluoroquinolones,Quinolones"	"J01MA15,QJ01MA15"	"Quinolone antibacterials"	"Fluoroquinolones"	"gemifl"	"factiv,gemifioxacin,gemifloxacine,gemifloxacino,gemifloxacinum"	0.32	"g"	0.2	"g"	"35814-3,35815-0,35816-8,41697-4"
 "GEN"	3467	"Gentamicin"	"Aminoglycosides"	"D06AX07,J01GB03,QA07AA91,QD06AX07,QG01AA91,QG51AA04,QJ01GB03,QJ51GB03,QS01AA11,QS02AA14,QS03AA06,S01AA11,S02AA14,S03AA06"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"cn,ge1000,ge2000,gen,gen128,gen500,gent,genta1,gentam,gm"	"centicin,cidomycin,garamicin,garamycin,gentacycol,gentamicina,gentamicine,gentamicins,gentamicinum,gentamycins,gentamycinum,gentocin,lyramycin,oksitselanim,septigen,septocin"			0.24	"g"	"101494-3,13561-6,13562-4,15106-8,18928-2,18929-0,22746-2,22747-0,266-7,267-5,268-3,269-1,31091-2,31092-0,31093-8,35668-3,35817-6,3663-2,3664-0,3665-7,39082-3,47109-4,50630-3,59379-8,7016-9,7017-7,7018-5,80971-5,88111-0,89481-6"
 "GEH"		"Gentamicin-high"	"Aminoglycosides"	"NA"			"gehi,gehl,genta high,gentamicin high"	"NA"					"18929-0,35817-6,7017-7,7018-5"
-"GEP"	25101874	"Gepotidacin"	"Other antibacterials"	"J01XX13,QJ01XX13"			"NA"	"gepotidacina,gepotidacine"					"NA"
-"GRX"	72474	"Grepafloxacin"	"Fluoroquinolones"	"J01MA11,QJ01MA11"	"Quinolone antibacterials"	"Fluoroquinolones"	"grep,grepaf"	"grepafloxacine,grepafloxacino,lungaskin,raxar,vaxar"	0.4	"g"			"21316-5,23638-0,23639-8,35818-4"
-"GRI"	441140	"Griseofulvin"	"Antifungals/antimycotics"	"D01AA08,D01BA01,QD01AA08,QD01BA01"			"NA"	"amudane,delmofulvina,epigriseofulvin,fulcin,fulcine,fulvicin,fulvidex,fulvina,fulvinil,fulvistatin,fungivin,greosin,gresfeed,gricin,grifulin,grifulvin,grisactin,griscofulvin,grisefuline,griseo,griseofulviin,griseofulvina,griseofulvine,griseofulvinum,griseomix,griseostatin,grisetin,grisofulvin,grisovin,grisowen,grizeofulvin,grysio,guservin,lamoryl,likuden,likunden,murfulvin,poncyl,spiro,spirofulvin,xuanjing"	0.5	"g"			"12402-4,54200-1,54201-9,54202-7"
+"GEP"	25101874	"Gepotidacin"	"Other"	"J01XX13,QJ01XX13"			"NA"	"gepotidacina,gepotidacine"					"NA"
+"GRX"	72474	"Grepafloxacin"	"Fluoroquinolones,Quinolones"	"J01MA11,QJ01MA11"	"Quinolone antibacterials"	"Fluoroquinolones"	"grep,grepaf"	"grepafloxacine,grepafloxacino,lungaskin,raxar,vaxar"	0.4	"g"			"21316-5,23638-0,23639-8,35818-4"
+"GRI"	441140	"Griseofulvin"	"Antifungals"	"D01AA08,D01BA01,QD01AA08,QD01BA01"			"NA"	"amudane,delmofulvina,epigriseofulvin,fulcin,fulcine,fulvicin,fulvidex,fulvina,fulvinil,fulvistatin,fungivin,greosin,gresfeed,gricin,grifulin,grifulvin,grisactin,griscofulvin,grisefuline,griseo,griseofulviin,griseofulvina,griseofulvine,griseofulvinum,griseomix,griseostatin,grisetin,grisofulvin,grisovin,grisowen,grizeofulvin,grysio,guservin,lamoryl,likuden,likunden,murfulvin,poncyl,spiro,spirofulvin,xuanjing"	0.5	"g"			"12402-4,54200-1,54201-9,54202-7"
 "HAB"	175989	"Habekacin"	"Aminoglycosides"	"NA"			"NA"	"amikafur,amikan,amitrex,arikayce,biklin,biodacyn,chemacin,fabianol,habekacinxsulfate,likacin,pierami"					"NA"
-"HCH"	11979956	"Hachimycin"	"Antifungals/antimycotics"	"D01AA03,G01AA06,J02AA02,QD01AA03,QG01AA06,QJ02AA02"	"Antimycotics for systemic use"	"Antibiotics"	"NA"	"cabimicina,hachimicina,hachimycine,hachimycinum,trichomycinum,trichonat"					"NA"
-"HET"	443387	"Hetacillin"	"Beta-lactams/penicillins"	"J01CA18,QJ01CA18"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"hetaci"	"etacillina,hetacilina,hetacilline,hetacillinum,natacillin,phenazacillin,versapen,versatrex"	2	"g"			"18931-6,274-1,275-8,276-6,277-4"
+"HCH"	11979956	"Hachimycin"	"Antifungals"	"D01AA03,G01AA06,J02AA02,QD01AA03,QG01AA06,QJ02AA02"	"Antimycotics for systemic use"	"Antibiotics"	"NA"	"cabimicina,hachimicina,hachimycine,hachimycinum,trichomycinum,trichonat"					"NA"
+"HET"	443387	"Hetacillin"	"Penicillins,Beta-lactams"	"J01CA18,QJ01CA18"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"hetaci"	"etacillina,hetacilina,hetacilline,hetacillinum,natacillin,phenazacillin,versapen,versatrex"	2	"g"			"18931-6,274-1,275-8,276-6,277-4"
 "HYG"	56928061	"Hygromycin"	"Aminoglycosides"	"NA"			"NA"	"antihelmycin,destomysin,hyanthelmix,hygromix,hygrovectine,hygrovetine"					"NA"
 "IBX"		"Ibrexafungerp"	"Antifungals"	"J02AX07,QJ02AX07"			"NA"	"NA"					"NA"
-"ICL"	213043	"Iclaprim"	"Other antibacterials"	"J01EA03,QJ01EA03"			"iclapr"	"iclaprime,mersarex"					"73597-7,73619-9,73642-1"
-"IPM"	104838	"Imipenem"	"Carbapenems"	"J01DH51,QJ01DH51"	"Other beta-lactam antibacterials"	"Carbapenems"	"imci,imi,imip,imip32,imipen,imp"	"imipemide,imipenemum,imipenen,primaxin,recarbrio,tienam,tienamycin"			2	"g"	"101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8"
-"IPE"		"Imipenem/EDTA"	"Carbapenems"	"NA"			"NA"	"NA"					"35819-2,54170-6,54171-4,54172-2"
-"IMR"		"Imipenem/relebactam"	"Carbapenems"	"J01DH56,QJ01DH56"			"NA"	"NA"			2	"g"	"85424-0,93232-7,96372-8"
-"ISV"	6918485	"Isavuconazole"	"Antifungals/antimycotics"	"J02AC05,QJ02AC05"			"isav"	"benzonitrile,ravuconazole"	0.2	"g"	0.2	"g"	"85381-2,88887-5"
+"ICL"	213043	"Iclaprim"	"Trimethoprims"	"J01EA03,QJ01EA03"			"iclapr"	"iclaprime,mersarex"					"73597-7,73619-9,73642-1"
+"IPM"	104838	"Imipenem"	"Carbapenems,Beta-lactams"	"J01DH51,QJ01DH51"	"Other beta-lactam antibacterials"	"Carbapenems"	"imci,imi,imip,imip32,imipen,imp"	"imipemide,imipenemum,imipenen,primaxin,recarbrio,tienam,tienamycin"			2	"g"	"101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8"
+"IPE"		"Imipenem/EDTA"	"Carbapenems,Beta-lactams"	"NA"			"NA"	"NA"					"35819-2,54170-6,54171-4,54172-2"
+"IMR"		"Imipenem/relebactam"	"Carbapenems,Beta-lactams,Beta-lactamase inhibitors"	"J01DH56,QJ01DH56"			"NA"	"NA"			2	"g"	"85424-0,93232-7,96372-8"
+"ISV"	6918485	"Isavuconazole"	"Antifungals"	"J02AC05,QJ02AC05"			"isav"	"benzonitrile,ravuconazole"	0.2	"g"	0.2	"g"	"85381-2,88887-5"
 "ISE"	3037209	"Isepamicin"	"Aminoglycosides"	"J01GB11,QJ01GB11"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"isepam"	"isepacin,isepalline,isepamicina,isepamicine,isepamicinsulphate,isepamicinum"			0.4	"g"	"32381-6,35820-0,35821-8,55680-3"
-"ISO"	3760	"Isoconazole"	"Antifungals/antimycotics"	"D01AC05,G01AF07,QD01AC05,QG01AF07"	"Antimycotics for topic use"	"Triazole derivatives"	"NA"	"isoconazol,isoconazolum,travogen"					"55681-1,55682-9,55683-7,55684-5"
+"ISO"	3760	"Isoconazole"	"Antifungals"	"D01AC05,G01AF07,QD01AC05,QG01AF07"	"Antimycotics for topic use"	"Triazole derivatives"	"NA"	"isoconazol,isoconazolum,travogen"					"55681-1,55682-9,55683-7,55684-5"
 "INH"	3767	"Isoniazid"	"Antimycobacterials"	"J04AC01,QJ04AC01"	"Drugs for treatment of tuberculosis"	"Hydrazides"	"inh,isonia"	"abdizide,acetylisoniazide,andrazide,anidrasona,antimicina,antituberkulosum,armacide,armazid,armazide,atcotibine,azuren,cedin,cemidon,chemiazid,chemidon,continazine,cortinazine,cotinazin,cotinizin,defonin,dianicotyl,dibutin,diforin,dinacrin,dinocrin,ditubin,ebidene,eralon,ertuban,eutizon,evalon,fetefu,fimalene,hidranizil,hidrasonil,hidrulta,hidrun,hycozid,hydra,hydrazid,hyozid,hyzyd,idrazil,inizid,ipcazide,iscotin,isidrina,ismazide,isobicina,isocid,isocidene,isocotin,isohydrazide,isokin,isolyn,isonerit,isonex,isoniacid,isoniazida,isoniazide,isoniazidum,isonicazide,isonicid,isonico,isonicotan,isonicotil,isonicotinhydrazid,isonicotinohydrazide,isonide,isonidrin,isonikazid,isonilex,isonin,isonindon,isonirit,isoniton,isonizida,isonizide,isotamine,isotebe,isotebezid,isotinyl,isozid,isozide,isozyd,laniazid,laniozid,mayambutol,mybasan,neoteben,neoxin,neumandin,nevin,niadrin,nicazide,nicetal,nicizina,niconyl,nicotibina,nicotibine,nicotisan,nicozide,nidaton,nidrazid,nikozid,niplen,nitadon,niteban,nitebannsc,nydrazid,nyscozid,pelazid,percin,phthisen,preparation,pycazide,pyreazid,pyricidin,pyridicin,pyrizidin,raumanon,razide,retozide,rifater,rimicid,rimifon,rimiphone,rimitsid,robiselin,robisellin,roxifen,sanohidrazina,sauterazid,sauterzid,stanozide,tebecid,tebenic,tebexin,tebilon,tebos,teebaconin,tekazin,tibazide,tibemid,tibiazide,tibinide,tibison,tibivis,tibizide,tibusan,tisin,tisiodrazida,tizide,tubazid,tubazide,tubeco,tubecotubercid,tuberian,tubicon,tubilysin,tubizid,tubomel,tyvid,unicocyde,unicozyde,vazadrine,vederon,zidafimia,zinadon,zonazide"	0.3	"g"	0.3	"g"	"18934-0,20383-6,23947-5,25217-1,25218-9,25219-7,25451-6,26756-7,286-5,287-3,288-1,289-9,29315-9,3697-0,40371-7,42649-4,42650-2,42651-0,45215-1,48171-3,48172-1,55685-2,7020-1,89488-1"
-"IST"		"Isoniazid/sulfamethoxazole/trimethoprim/pyridoxine"	"Antimycobacterials"	"NA"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
-"ITR"	3793	"Itraconazole"	"Antifungals/antimycotics"	"J02AC02,QJ02AC02"	"Antimycotics for systemic use"	"Triazole derivatives"	"itra,itraco"	"candistat,canditral,cladosal,fungitraxx,intraconazole,itraconazol,itraconazolo,itraconazolum,itraconzaole,itrafungol,itralek,itrizole,lozanoc,onmel,sempera,sporamelt,sporanox,sporonox,traconal,triasporin"	0.2	"g"	0.2	"g"	"10989-2,12392-7,25258-5,25452-4,27081-9,32184-4,32185-1,32603-3,54179-7,7021-9,80531-7"
-"JOS"	5282165	"Josamycin"	"Macrolides/lincosamides"	"J01FA07,QJ01FA07"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"josamy"	"jomybel,josamicina,josamycine,josamycinum"	2	"g"			"25597-6,25702-2,41698-2,41699-0"
+"IST"		"Isoniazid/sulfamethoxazole/trimethoprim/pyridoxine"	"Trimethoprims,Sulfonamides,Antimycobacterials"	"NA"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
+"ITR"	3793	"Itraconazole"	"Antifungals"	"J02AC02,QJ02AC02"	"Antimycotics for systemic use"	"Triazole derivatives"	"itra,itraco"	"candistat,canditral,cladosal,fungitraxx,intraconazole,itraconazol,itraconazolo,itraconazolum,itraconzaole,itrafungol,itralek,itrizole,lozanoc,onmel,sempera,sporamelt,sporanox,sporonox,traconal,triasporin"	0.2	"g"	0.2	"g"	"10989-2,12392-7,25258-5,25452-4,27081-9,32184-4,32185-1,32603-3,54179-7,7021-9,80531-7"
+"JOS"	5282165	"Josamycin"	"Macrolides"	"J01FA07,QJ01FA07"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"josamy"	"jomybel,josamicina,josamycine,josamycinum"	2	"g"			"25597-6,25702-2,41698-2,41699-0"
 "KAN"	6032	"Kanamycin"	"Aminoglycosides"	"A07AA08,J01GB04,QA07AA08,QJ01GB04,QS01AA24,S01AA24"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"hlk,k,kan,kana,kanamy,km"	"kanamicina,kanamycine,kanamycins,kanamycinum,kantrex,klebcil"	3	"g"	1	"g"	"18935-7,18936-5,23609-1,23889-9,25182-7,25213-0,25214-8,290-7,291-5,292-3,293-1,3698-8,3699-6,3700-2,42652-8,47395-9,49080-5,7022-7,7023-5,7024-3,88002-1,88705-9,89482-4"
 "KAH"		"Kanamycin-high"	"Aminoglycosides"	"NA"			"k_h,kahl"	"NA"					"18936-5,7023-5,7024-3"
 "KAC"		"Kanamycin/cephalexin"	"Aminoglycosides"	"NA"			"NA"	"NA"					"NA"
-"KET"	456201	"Ketoconazole"	"Antifungals/antimycotics"	"D01AC08,G01AF11,H02CA03,J02AB02,QD01AC08,QG01AF11,QH02CA03,QJ02AB02"	"Antimycotics for systemic use"	"Imidazole derivatives"	"keto,ketoco,ktc"	"brizoral,ethanone,extina,fungarest,fungoral,ketaconazole,ketocanazole,ketoconazol,ketoconazolum,ketodan,ketoderm,ketoisdin,ketozole,kuric,levoketoconazole,nizoral,normocort,panfungol,piperazine,recorlev,sebazole,teryzolin,terzolin,tocris,xolegel"	0.6	"g"			"10990-0,12393-5,18937-3,25259-3,294-9,295-6,296-4,297-2,60091-6,60092-4,7025-0"
-"KIT"		"Kitasamycin"	"Macrolides/lincosamides"	"QJ01FA93"			"leucomycin"	"NA"					"NA"
-"LAS"	5360807	"Lasalocid"	"Other antibacterials"	"QP51BB02"			"NA"	"avatec,bovate,bovatec,lasalocide,lasalocido,lasalocidsalt,lasalocidum"					"87598-9"
-"LSC"	71528768	"Lascufloxacin"	"Fluoroquinolones"	"J01MA25,QJ01MA25"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"lasvic"	75	"mg"			"NA"
-"LTM"	47499	"Latamoxef"	"Cephalosporins (3rd gen.)"	"J01DD06,QJ01DD06"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"mox,moxa,moxalactam"	"dilatamoxef,festamoxin,lamoxactam,latamoxefum,morrhuate,moxalactamsalt,moxam,shiomarin"			4	"g"	"NA"
-"LMU"	25185057	"Lefamulin"	"Other antibacterials"	"J01XX12,QJ01XX12"			"NA"	"lefamulinacetate,xenleta"					"85425-7,99281-8"
-"LEN"	65646	"Lenampicillin"	"Beta-lactams/penicillins"	"NA"			"NA"	"lenampicilina,lenampicilline,lenampicillinum,takacillin,valacillin,varacillin"					"NA"
-"LVX"	149096	"Levofloxacin"	"Fluoroquinolones"	"J01MA12,QJ01MA12,QS01AE05,S01AE05"	"Quinolone antibacterials"	"Fluoroquinolones"	"le,lev,levo,levofl,lvx"	"aeroquin,cravit,dextrofloxacin,dynaquin,elequine,iquix,levaquin,levofiexacin,levofloxacine,levofloxacino,levofloxacinum,loxof,ofloxcacin,oftaquix,quinsair,quixin,tavanic,unibiotic,venaxan"	0.5	"g"	0.5	"g"	"101501-5,20396-8,20629-2,21367-8,21368-6,30532-6,30533-4,48173-9,53716-7,7026-8,76040-5,76041-3,76042-1"
-"LEO"		"Levofloxacin/ornidazole"	"Fluoroquinolones"	"J01RA05,QJ01RA05"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"LND"	9850038	"Levonadifloxacin"	"Fluoroquinolones"	"J01MA24,QJ01MA24"			"NA"	"NA"					"NA"
-"LSP"		"Linco-spectin"	"Other antibacterials"	"NA"			"lincomycin/spectinomycin"	"NA"					"NA"
-"LIN"	3000540	"Lincomycin"	"Macrolides/lincosamides"	"J01FF02,QJ01FF02,QJ51FF02"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"linc,lincom"	"albiotic,bactramycin,cillimycin,frademicina,jiemycin,lincocin,lincogap,lincolcina,lincolnensin,lincomicina,lincomix,lincomycine,lincomycinum,lincomyocin,lincorex,linocin,mycivin"	1.8	"g"	1.8	"g"	"18938-1,298-0,299-8,300-4,301-2,41700-6,87597-1"
+"KET"	456201	"Ketoconazole"	"Antifungals"	"D01AC08,G01AF11,H02CA03,J02AB02,QD01AC08,QG01AF11,QH02CA03,QJ02AB02"	"Antimycotics for systemic use"	"Imidazole derivatives"	"keto,ketoco,ktc"	"brizoral,ethanone,extina,fungarest,fungoral,ketaconazole,ketocanazole,ketoconazol,ketoconazolum,ketodan,ketoderm,ketoisdin,ketozole,kuric,levoketoconazole,nizoral,normocort,panfungol,piperazine,recorlev,sebazole,teryzolin,terzolin,tocris,xolegel"	0.6	"g"			"10990-0,12393-5,18937-3,25259-3,294-9,295-6,296-4,297-2,60091-6,60092-4,7025-0"
+"KIT"		"Kitasamycin"	"Macrolides"	"QJ01FA93"			"leucomycin"	"NA"					"NA"
+"LAS"	5360807	"Lasalocid"	"Other"	"QP51BB02"			"NA"	"avatec,bovate,bovatec,lasalocide,lasalocido,lasalocidsalt,lasalocidum"					"87598-9"
+"LSC"	71528768	"Lascufloxacin"	"Fluoroquinolones,Quinolones"	"J01MA25,QJ01MA25"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"lasvic"	75	"mg"			"NA"
+"LTM"	47499	"Latamoxef"	"Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams"	"J01DD06,QJ01DD06"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"mox,moxa,moxalactam"	"dilatamoxef,festamoxin,lamoxactam,latamoxefum,morrhuate,moxalactamsalt,moxam,shiomarin"			4	"g"	"NA"
+"LMU"	25185057	"Lefamulin"	"Other"	"J01XX12,QJ01XX12"			"NA"	"lefamulinacetate,xenleta"					"85425-7,99281-8"
+"LEN"	65646	"Lenampicillin"	"Penicillins,Beta-lactams"	"NA"			"NA"	"lenampicilina,lenampicilline,lenampicillinum,takacillin,valacillin,varacillin"					"NA"
+"LVX"	149096	"Levofloxacin"	"Fluoroquinolones,Quinolones"	"J01MA12,QJ01MA12,QS01AE05,S01AE05"	"Quinolone antibacterials"	"Fluoroquinolones"	"le,lev,levo,levofl,lvx"	"aeroquin,cravit,dextrofloxacin,dynaquin,elequine,iquix,levaquin,levofiexacin,levofloxacine,levofloxacino,levofloxacinum,loxof,ofloxcacin,oftaquix,quinsair,quixin,tavanic,unibiotic,venaxan"	0.5	"g"	0.5	"g"	"101501-5,20396-8,20629-2,21367-8,21368-6,30532-6,30533-4,48173-9,53716-7,7026-8,76040-5,76041-3,76042-1"
+"LEO"		"Levofloxacin/ornidazole"	"Fluoroquinolones,Quinolones"	"J01RA05,QJ01RA05"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"LND"	9850038	"Levonadifloxacin"	"Fluoroquinolones,Quinolones"	"J01MA24,QJ01MA24"			"NA"	"NA"					"NA"
+"LSP"		"Linco-spectin"	"Other"	"NA"			"lincomycin/spectinomycin"	"NA"					"NA"
+"LIN"	3000540	"Lincomycin"	"Lincosamides"	"J01FF02,QJ01FF02,QJ51FF02"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"linc,lincom"	"albiotic,bactramycin,cillimycin,frademicina,jiemycin,lincocin,lincogap,lincolcina,lincolnensin,lincomicina,lincomix,lincomycine,lincomycinum,lincomyocin,lincorex,linocin,mycivin"	1.8	"g"	1.8	"g"	"18938-1,298-0,299-8,300-4,301-2,41700-6,87597-1"
 "LNZ"	441401	"Linezolid"	"Oxazolidinones"	"J01XX08,QJ01XX08"	"Other antibacterials"	"Other antibacterials"	"line,linezo,lnz,lz,lzd"	"desfluorolinezolid,linezoid,linezolidum,zivoxid,zyvox,zyvoxa,zyvoxam,zyvoxid"	1.2	"g"	1.2	"g"	"29254-0,29255-7,29258-1,33332-8,34202-2,41500-0,80609-1,88706-7,96111-0"
-"LFE"		"Linoprist-flopristin"	"Other antibacterials"	"NA"			"linflo"	"NA"					"NA"
-"LOM"	3948	"Lomefloxacin"	"Fluoroquinolones"	"J01MA07,QJ01MA07,QS01AE04,S01AE04"	"Quinolone antibacterials"	"Fluoroquinolones"	"lmf,lom,lome,lomefl"	"bareon,logiflox,lomebact,lomefloxacine,lomefloxacino,lomefloxacinum,maxaquin,maxaquine,mazaquin,okacin,okacyn,uniquin"	0.4	"g"			"18939-9,302-0,303-8,304-6,305-3,41701-4"
-"LOR"	5284585	"Loracarbef"	"Cephalosporins (2nd gen.)"	"J01DC08,QJ01DC08"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"lora,loraca"	"carbac,lorabid,loracarbefum,lorafem,lorbef,loribid"	0.6	"g"			"18940-7,306-1,307-9,308-7,309-5,7027-6"
+"LFE"		"Linoprist-flopristin"	"Other"	"NA"			"linflo"	"NA"					"NA"
+"LOM"	3948	"Lomefloxacin"	"Fluoroquinolones,Quinolones"	"J01MA07,QJ01MA07,QS01AE04,S01AE04"	"Quinolone antibacterials"	"Fluoroquinolones"	"lmf,lom,lome,lomefl"	"bareon,logiflox,lomebact,lomefloxacine,lomefloxacino,lomefloxacinum,maxaquin,maxaquine,mazaquin,okacin,okacyn,uniquin"	0.4	"g"			"18939-9,302-0,303-8,304-6,305-3,41701-4"
+"LOR"	5284585	"Loracarbef"	"Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams"	"J01DC08,QJ01DC08"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"lora,loraca"	"carbac,lorabid,loracarbefum,lorafem,lorbef,loribid"	0.6	"g"			"18940-7,306-1,307-9,308-7,309-5,7027-6"
 "LYM"	54707177	"Lymecycline"	"Tetracyclines"	"J01AA04,QJ01AA04"	"Tetracyclines"	"Tetracyclines"	"NA"	"armyl,chlortetracyclin,ciclisin,ciclolysal,ciclolysine,eficiclina,infaciclina,limeciclina,lisinbiotic,lymecyclinum,mucomycin,ntetracycline,tetralisal,tetralysal,vebicyclysal"	0.6	"g"	0.6	"g"	"18941-5,310-3,311-1,312-9,313-7"
-"MNA"	1292	"Mandelic acid"	"Other antibacterials"	"B05CA06,J01XX06,QB05CA06,QJ01XX06"	"Other antibacterials"	"Other antibacterials"	"NA"	"amygdalate,mandelsaeure,paramandelate,phenylglycolate,phenylhydroxyacetate,uromaline"	12	"g"			"NA"
+"MNA"	1292	"Mandelic acid"	"Other"	"B05CA06,J01XX06,QB05CA06,QJ01XX06"	"Other antibacterials"	"Other antibacterials"	"NA"	"amygdalate,mandelsaeure,paramandelate,phenylglycolate,phenylhydroxyacetate,uromaline"	12	"g"			"NA"
 "MGX"		"Manogepix"	"Antifungals"	"NA"			"NA"	"NA"					"NA"
-"MAR"	60651	"Marbofloxacin"	"Fluoroquinolones"	"QJ01MA93"			"marbof"	"marbocyl,marbofloxacine,marbofloxacino,marbofloxacinum,marboquin,zeniquin"					"73596-9,73618-1,73641-3"
-"MEC"	36273	"Mecillinam"	"Beta-lactams/penicillins"	"J01CA11,QJ01CA11"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"amdinocillin,mecill"	"amdinocillin,coactin,hexacillin,mecilinamo,mecillinamum,selexidin"			1.2	"g"	"NA"
-"MEL"	71306732	"Meleumycin"	"Macrolides/lincosamides"	"NA"			"NA"	"NA"					"NA"
-"MEM"	441130	"Meropenem"	"Carbapenems"	"J01DH02,QJ01DH02"	"Other beta-lactam antibacterials"	"Carbapenems"	"mem,mer,mero,merope,mp,mrp"	"meronem,meropen,meropenemum,merrem"			3	"g"	"101222-8,101488-5,101489-3,18943-1,41406-0,6651-4,6652-2,6653-0,6654-8,7029-2,85426-5,85427-3,88892-5,90980-4"
-"MNC"		"Meropenem/nacubactam"	"Carbapenems"	"NA"			"NA"	"NA"					"NA"
-"MEV"		"Meropenem/vaborbactam"	"Carbapenems"	"J01DH52,QJ01DH52"	"Other beta-lactam antibacterials"	"Carbapenems"	"NA"	"NA"			3	"g"	"101222-8,101489-3,85427-3,88892-5,90980-4"
-"MES"	176886	"Mesulfamide"	"Other antibacterials"	"NA"			"NA"	"mesulfamida,mesulfamido,mesulfamidum"					"NA"
+"MAR"	60651	"Marbofloxacin"	"Fluoroquinolones,Quinolones"	"QJ01MA93"			"marbof"	"marbocyl,marbofloxacine,marbofloxacino,marbofloxacinum,marboquin,zeniquin"					"73596-9,73618-1,73641-3"
+"MEC"	36273	"Mecillinam"	"Penicillins,Beta-lactams"	"J01CA11,QJ01CA11"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"amdinocillin,mecill"	"amdinocillin,coactin,hexacillin,mecilinamo,mecillinamum,selexidin"			1.2	"g"	"NA"
+"MEL"	71306732	"Meleumycin"	"Macrolides"	"NA"			"NA"	"NA"					"NA"
+"MEM"	441130	"Meropenem"	"Carbapenems,Beta-lactams"	"J01DH02,QJ01DH02"	"Other beta-lactam antibacterials"	"Carbapenems"	"mem,mer,mero,merope,mp,mrp"	"meronem,meropen,meropenemum,merrem"			3	"g"	"101222-8,101488-5,101489-3,18943-1,41406-0,6651-4,6652-2,6653-0,6654-8,7029-2,85426-5,85427-3,88892-5,90980-4"
+"MNC"		"Meropenem/nacubactam"	"Carbapenems,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"NA"	"NA"					"NA"
+"MEV"		"Meropenem/vaborbactam"	"Carbapenems,Beta-lactams,Beta-lactamase inhibitors"	"J01DH52,QJ01DH52"	"Other beta-lactam antibacterials"	"Carbapenems"	"NA"	"NA"			3	"g"	"101222-8,101489-3,85427-3,88892-5,90980-4"
+"MES"	176886	"Mesulfamide"	"Other"	"NA"			"NA"	"mesulfamida,mesulfamido,mesulfamidum"					"NA"
 "MTC"	54675785	"Metacycline"	"Tetracyclines"	"J01AA05,QJ01AA05"	"Tetracyclines"	"Tetracyclines"	"methcy"	"bialatan,metaciclina,metacyclinum,methacyclin,methacycline,methacyclinum,methylenecycline,physiomycine,rondomycin"	0.6	"g"			"NA"
-"MTM"	6713928	"Metampicillin"	"Beta-lactams/penicillins"	"J01CA14,QJ01CA14"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"blomopen,bonopen,celinmicina,elatocilline,filorex,magnipen,metambac,metampen,metampicilina,metampicillina,metampicilline,metampicillinsalt,metampicillinum,micinovo,ocelina,pangocilin,probiotic,relyothenate,ruticina,rutizina,sedomycin,serfabiotic,suvipen,viderpen,viderpin,vioplex"	1.5	"g"	1.5	"g"	"NA"
-"MTH"	4101	"Methenamine"	"Other antibacterials"	"J01XX05,QJ01XX05"	"Other antibacterials"	"Other antibacterials"	"NA"	"aminoform,aminoformaldehyde,ammoform,ammonioformaldehyde,antihydral,carin,cystamin,cystex,cystogen,duirexol,esametilentetramina,formamine,formin,grasselerator,heterin,hexaform,hexaloids,hexamethylamine,hexamethylenamine,hexamethyleneamine,hexamethylentetramin,hexamine,hexaminum,hexasan,hexilmethylenamine,metenamina,metenamine,methamin,methamine,methenamin,methenaminum,metramine,naphthamine,pellurin,resotropin,uramin,urasal,uratrine,urisol,uritone,urodeine,urotropin,urotropine,vesaloin,xametrin"	3	"g"			"NA"
-"MET"	6087	"Meticillin"	"Beta-lactams/penicillins"	"J01CF03,QJ01CF03,QJ51CF03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"methic,meti"	"belfacillin,celbenin,celpilline,cinopenil,dimocillin,estafcilina,flabelline,lucopenin,metacillin,methcillin,methicillin,methicillinanhydrous,methicillinhydrate,methicillinsalt,methicillinum,methycillin,meticilina,meticillina,meticilline,meticillinsalt,meticillinum,penaureus,penysol,staficyn,staphcillin,synticillin"			4	"g"	"NA"
-"MTP"	68590	"Metioprim"	"Other antibacterials"	"NA"			"NA"	"methioprim,metioprima,metioprime,metioprimum"					"NA"
-"MXT"	3047729	"Metioxate"	"Fluoroquinolones"	"NA"			"NA"	"metioxato,metioxatum"					"NA"
-"MTR"	4173	"Metronidazole"	"Other antibacterials"	"A01AB17,D06BX01,G01AF01,J01XD01,P01AB01,QA01AB17,QD06BX01,QG01AF01,QJ01XD01,QP51CA01"	"Other antibacterials"	"Imidazole derivatives"	"metr,metron,mnz"	"acromona,anagiardil,arilin,atrivyl,bexon,clont,danizol,deflamon,donnan,efloran,elyzol,entizol,eumin,flagemona,flagesol,flagil,flagyl,flazol,flegyl,florazole,fossyol,giatricol,gineflavir,givagil,hydroxydimetridazole,hydroxymetronidazole,izoklion,klion,klont,mepagyl,meronidal,metric,metrolag,metrolyl,metromidol,metronidazolo,metronidazolum,metroplex,metrotop,mexibol,monagyl,monasin,nalox,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosaced,rosased,sanatrichom,satric,takimetol,trichazol,trichex,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,trikacide,trikamon,trikhopol,trikojol,trikozol,trimeks,trivazol,vagilen,vagimid,vandazole,vertisal,wagitran,zadstat,zidoval"	2	"g"	1.5	"g"	"10991-8,18946-4,326-9,327-7,328-5,329-3,7031-8"
-"MEZ"	656511	"Mezlocillin"	"Beta-lactams/penicillins"	"J01CA10,QJ01CA10"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"mez,mezl,mezlo,mz"	"baycipen,baypen,mezlin,mezlocilina,mezlocilline,mezlocillinsalt,mezlocillinum,multocillin"			6	"g"	"18947-2,330-1,331-9,332-7,333-5,3820-8,41702-2,54194-6,54195-3,54196-1"
-"MSU"		"Mezlocillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			"mezsul"	"NA"					"54194-6,54195-3,54196-1"
-"MIF"	477468	"Micafungin"	"Antifungals/antimycotics"	"J02AX05,QJ02AX05"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"mica,micafu"	"fungard,funguard,micafungina,micafunginsalt,mycamine"			0.1	"g"	"53812-4,58418-5,65340-2,85048-7"
-"MCZ"	4189	"Miconazole"	"Antifungals/antimycotics"	"A01AB09,A07AC01,D01AC02,G01AF04,J02AB01,QA01AB09,QA07AC01,QD01AC02,QG01AF04,QJ02AB01,QS02AA13,S02AA13"	"Antimycotics for systemic use"	"Imidazole derivatives"	"mico"	"aflorix,albistat,andergin,brentan,conofite,dactarin,florid,micantin,miconazol,miconazolo,miconazolum,micozole,minostate,monazole,monista,monistat,oravig,vusion,zimybase,zimycan"	0.2	"g"	1	"g"	"17278-3,25607-3,25722-0,54180-5,55686-0"
+"MTM"	6713928	"Metampicillin"	"Penicillins,Beta-lactams"	"J01CA14,QJ01CA14"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"blomopen,bonopen,celinmicina,elatocilline,filorex,magnipen,metambac,metampen,metampicilina,metampicillina,metampicilline,metampicillinsalt,metampicillinum,micinovo,ocelina,pangocilin,probiotic,relyothenate,ruticina,rutizina,sedomycin,serfabiotic,suvipen,viderpen,viderpin,vioplex"	1.5	"g"	1.5	"g"	"NA"
+"MTH"	4101	"Methenamine"	"Other"	"J01XX05,QJ01XX05"	"Other antibacterials"	"Other antibacterials"	"NA"	"aminoform,aminoformaldehyde,ammoform,ammonioformaldehyde,antihydral,carin,cystamin,cystex,cystogen,duirexol,esametilentetramina,formamine,formin,grasselerator,heterin,hexaform,hexaloids,hexamethylamine,hexamethylenamine,hexamethyleneamine,hexamethylentetramin,hexamine,hexaminum,hexasan,hexilmethylenamine,metenamina,metenamine,methamin,methamine,methenamin,methenaminum,metramine,naphthamine,pellurin,resotropin,uramin,urasal,uratrine,urisol,uritone,urodeine,urotropin,urotropine,vesaloin,xametrin"	3	"g"			"NA"
+"MET"	6087	"Meticillin"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"J01CF03,QJ01CF03,QJ51CF03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"methic,meti"	"belfacillin,celbenin,celpilline,cinopenil,dimocillin,estafcilina,flabelline,lucopenin,metacillin,methcillin,methicillin,methicillinanhydrous,methicillinhydrate,methicillinsalt,methicillinum,methycillin,meticilina,meticillina,meticilline,meticillinsalt,meticillinum,penaureus,penysol,staficyn,staphcillin,synticillin"			4	"g"	"NA"
+"MTP"	68590	"Metioprim"	"Other"	"NA"			"NA"	"methioprim,metioprima,metioprime,metioprimum"					"NA"
+"MXT"	3047729	"Metioxate"	"Fluoroquinolones,Quinolones"	"NA"			"NA"	"metioxato,metioxatum"					"NA"
+"MTR"	4173	"Metronidazole"	"Other"	"A01AB17,D06BX01,G01AF01,J01XD01,P01AB01,QA01AB17,QD06BX01,QG01AF01,QJ01XD01,QP51CA01"	"Other antibacterials"	"Imidazole derivatives"	"metr,metron,mnz,mtz"	"acromona,anagiardil,arilin,atrivyl,bexon,clont,danizol,deflamon,donnan,efloran,elyzol,entizol,eumin,flagemona,flagesol,flagil,flagyl,flazol,flegyl,florazole,fossyol,giatricol,gineflavir,givagil,hydroxydimetridazole,hydroxymetronidazole,izoklion,klion,klont,mepagyl,meronidal,metric,metrolag,metrolyl,metromidol,metronidazolo,metronidazolum,metroplex,metrotop,mexibol,monagyl,monasin,nalox,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosaced,rosased,sanatrichom,satric,takimetol,trichazol,trichex,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,trikacide,trikamon,trikhopol,trikojol,trikozol,trimeks,trivazol,vagilen,vagimid,vandazole,vertisal,wagitran,zadstat,zidoval"	2	"g"	1.5	"g"	"10991-8,18946-4,326-9,327-7,328-5,329-3,7031-8"
+"MEZ"	656511	"Mezlocillin"	"Ureidopenicillins,Penicillins,Beta-lactams"	"J01CA10,QJ01CA10"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"mez,mezl,mezlo,mz"	"baycipen,baypen,mezlin,mezlocilina,mezlocilline,mezlocillinsalt,mezlocillinum,multocillin"			6	"g"	"18947-2,330-1,331-9,332-7,333-5,3820-8,41702-2,54194-6,54195-3,54196-1"
+"MSU"		"Mezlocillin/sulbactam"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"mezsul"	"NA"					"54194-6,54195-3,54196-1"
+"MIF"	477468	"Micafungin"	"Antifungals"	"J02AX05,QJ02AX05"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"mica,micafu"	"fungard,funguard,micafungina,micafunginsalt,mycamine"			0.1	"g"	"53812-4,58418-5,65340-2,85048-7"
+"MCZ"	4189	"Miconazole"	"Antifungals"	"A01AB09,A07AC01,D01AC02,G01AF04,J02AB01,QA01AB09,QA07AC01,QD01AC02,QG01AF04,QJ02AB01,QS02AA13,S02AA13"	"Antimycotics for systemic use"	"Imidazole derivatives"	"mico"	"aflorix,albistat,andergin,brentan,conofite,dactarin,florid,micantin,miconazol,miconazolo,miconazolum,micozole,minostate,monazole,monista,monistat,oravig,vusion,zimybase,zimycan"	0.2	"g"	1	"g"	"17278-3,25607-3,25722-0,54180-5,55686-0"
 "MCR"	3037206	"Micronomicin"	"Aminoglycosides"	"QS01AA22,S01AA22"			"micron"	"micromicin,micromycin,micronomicina,micronomicine,micronomicinum,sagamicin,santemycin"					"NA"
-"MID"	5282169	"Midecamycin"	"Macrolides/lincosamides"	"J01FA03,QJ01FA03"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"mideka"	"macropen,madecacine,medemycin,midecamicina,midecamycine,midecamycinum,midecin,momicine,myoxam,normicina,rubimycin"	1.2	"g"	1	"g"	"NA"
-"MIL"	37614	"Miloxacin"	"Fluoroquinolones"	"NA"			"amiflo"	"miloxacine,miloxacino,miloxacinum"					"NA"
+"MID"	5282169	"Midecamycin"	"Macrolides"	"J01FA03,QJ01FA03"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"mideka"	"macropen,madecacine,medemycin,midecamicina,midecamycine,midecamycinum,midecin,momicine,myoxam,normicina,rubimycin"	1.2	"g"	1	"g"	"NA"
+"MIL"	37614	"Miloxacin"	"Fluoroquinolones,Quinolones"	"NA"			"amiflo"	"miloxacine,miloxacino,miloxacinum"					"NA"
 "MNO"	54675783	"Minocycline"	"Tetracyclines"	"A01AB23,D10AF07,J01AA08,QA01AB23,QD10AF07,QJ01AA08"	"Tetracyclines"	"Tetracyclines"	"mc,mh,mi,min,mino,minocy,mn,mno"	"acnez,arestin,borymycin,dynacin,lederderm,minociclina,minocin,minocline,minocyclin,minocyclinum,minocyn,minomax,minomycin,mynocine,periocline,solodyn,vectrin,ximino"	1	"mg"	0.2	"g"	"18948-0,25225-4,334-3,335-0,336-8,337-6,34606-4,3822-4,49757-8,55156-4,7032-6"
-"MCM"	5282188	"Miocamycin"	"Macrolides/lincosamides"	"J01FA11,QJ01FA11"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"NA"	"acecamycin,macroral,miocamen,miocamycine,miokamycin,mosil,myocamicin,ponsinomycin"	1.2	"g"			"18949-8,338-4,339-2,340-0,341-8,55687-8"
-"MON"	23667299	"Monensin sodium"	"Other antibacterials"	"NA"			"NA"	"coban,elancoban,monelan,monensin,monensina,monensine,monensinum,monovet,romensin,rumensin"					"NA"
+"MCM"	5282188	"Miocamycin"	"Macrolides"	"J01FA11,QJ01FA11"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"NA"	"acecamycin,macroral,miocamen,miocamycine,miokamycin,mosil,myocamicin,ponsinomycin"	1.2	"g"			"18949-8,338-4,339-2,340-0,341-8,55687-8"
+"MON"	23667299	"Monensin sodium"	"Other"	"NA"			"NA"	"coban,elancoban,monelan,monensin,monensina,monensine,monensinum,monovet,romensin,rumensin"					"NA"
 "MRN"	70374	"Morinamide"	"Antimycobacterials"	"J04AK04,QJ04AK04"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"NA"	"morfazinamide,morfazinammide,morfgazinamide,morinamida,morinamidum,morphazinamid,morphazinamide,piazofolina,piazolin,piazolina"					"NA"
-"MFX"	152946	"Moxifloxacin"	"Fluoroquinolones"	"J01MA14,QJ01MA14,QS01AE07,S01AE07"	"Quinolone antibacterials"	"Fluoroquinolones"	"mox,moxi,moxifl,mxf"	"actira,actura,avalox,avelox,avolex,izilox,moxeza,moxifloxacine,moxifloxacino,octegra,vegamox,vigamox,zimoxin"	0.4	"g"	0.4	"g"	"31037-5,31039-1,31041-7,31043-3,41502-6,43751-7,45223-5,76043-9,76044-7,76045-4,80540-8,88707-5,93497-6,96112-8"
-"MUP"	446596	"Mupirocin"	"Other antibacterials"	"D06AX09,QD06AX09,QR01AX06,R01AX06"			"mup,mupi,mupiro"	"bactoderm,bactroban,centany,mupirocina,mupirocine,mupirocinum,plasimine,turixin"					"20389-3,35822-6,35823-4,60542-8,60543-6,7033-4"
-"NAC"	73386748	"Nacubactam"	"Beta-lactams/penicillins"	"NA"			"NA"	"NA"					"NA"
-"NAD"	4410	"Nadifloxacin"	"Fluoroquinolones"	"D10AF05,QD10AF05"			"NA"	"acuatim,nadifloxacine,nadifloxacino,nadifloxacinum,nadixa,nadoxin"					"NA"
-"NAF"	8982	"Nafcillin"	"Beta-lactams/penicillins"	"J01CF06,QJ01CF06"			"nafcil"	"nafcil,nafcilin,nafcilina,nafcillinanhydrous,nafcilline,nafcillinhydrate,nafcillinmonohydrate,nafcillinsalt,nafcillinum,naftopen,nallpen,naphcillin,naphthicillin,unipen"			3	"g"	"10993-4,18951-4,25232-0,346-7,347-5,348-3,349-1,41704-8"
-"ZWK"	117587595	"Nafithromycin"	"Macrolides/lincosamides"	"NA"			"NA"	"NA"					"NA"
+"MFX"	152946	"Moxifloxacin"	"Fluoroquinolones,Quinolones"	"J01MA14,QJ01MA14,QS01AE07,S01AE07"	"Quinolone antibacterials"	"Fluoroquinolones"	"mox,moxi,moxifl,mxf"	"actira,actura,avalox,avelox,avolex,izilox,moxeza,moxifloxacine,moxifloxacino,octegra,vegamox,vigamox,zimoxin"	0.4	"g"	0.4	"g"	"31037-5,31039-1,31041-7,31043-3,41502-6,43751-7,45223-5,76043-9,76044-7,76045-4,80540-8,88707-5,93497-6,96112-8"
+"MUP"	446596	"Mupirocin"	"Other"	"D06AX09,QD06AX09,QR01AX06,R01AX06"			"mup,mupi,mupiro"	"bactoderm,bactroban,centany,mupirocina,mupirocine,mupirocinum,plasimine,turixin"					"20389-3,35822-6,35823-4,60542-8,60543-6,7033-4"
+"NAC"	73386748	"Nacubactam"	"Beta-lactamase inhibitors"	"NA"			"NA"	"NA"					"NA"
+"NAD"	4410	"Nadifloxacin"	"Fluoroquinolones,Quinolones"	"D10AF05,QD10AF05"			"NA"	"acuatim,nadifloxacine,nadifloxacino,nadifloxacinum,nadixa,nadoxin"					"NA"
+"NAF"	8982	"Nafcillin"	"Penicillins,Beta-lactams"	"J01CF06,QJ01CF06"			"nafcil"	"nafcil,nafcilin,nafcilina,nafcillinanhydrous,nafcilline,nafcillinhydrate,nafcillinmonohydrate,nafcillinsalt,nafcillinum,naftopen,nallpen,naphcillin,naphthicillin,unipen"			3	"g"	"10993-4,18951-4,25232-0,346-7,347-5,348-3,349-1,41704-8"
+"ZWK"	117587595	"Nafithromycin"	"Macrolides"	"NA"			"NA"	"NA"					"NA"
 "NAL"	4421	"Nalidixic acid"	"Quinolones"	"J01MB02,QJ01MB02"	"Quinolone antibacterials"	"Other quinolones"	"na,nal,nalac,nali"	"amfonelinsaeure,baktogram,betaxina,chemiurin,cybis,dixiben,dixilina,dixinal,eucisten,eucistin,innoxalomn,innoxalon,jicsron,kusnarin,nalidicron,nalidixan,nalidixane,nalidixate,nalidixateanhydrous,nalidixic,nalidixin,nalidixinsaure,nalitucsan,nalix,nalurin,narigix,naxuril,negram,nevigramon,nicelate,nogram,poleon,sicmylon,specifen,specifin,unaserus,uralgin,uriben,uriclar,urisal,urodixin,uroman,uroneg,uronidix,uropan,wintomylon,wintron"	4	"g"			"NA"
 "NAL-S"		"Nalidixic acid screening test"	"Quinolones"	"NA"			"nal screen"	"NA"					"NA"
-"NAR"	65452	"Narasin"	"Other antibacterials"	"QP51BB04"			"narasi"	"monteban,narasine,narasino,narasinum,skycis"					"87570-8"
-"NEM"	11993740	"Nemonoxacin"	"Fluoroquinolones"	"J01MB08,QJ01MB08"	"Quinolone antibacterials"	"Other quinolones"	"NA"	"NA"					"NA"
+"NAR"	65452	"Narasin"	"Other"	"QP51BB04"			"narasi"	"monteban,narasine,narasino,narasinum,skycis"					"87570-8"
+"NEM"	11993740	"Nemonoxacin"	"Fluoroquinolones,Quinolones"	"J01MB08,QJ01MB08"	"Quinolone antibacterials"	"Other quinolones"	"NA"	"NA"					"NA"
 "NEO"	8378	"Neomycin"	"Aminoglycosides"	"A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,QA01AB08,QA07AA01,QB05CA09,QD06AX04,QJ01GB05,QR02AB01,QS01AA03,QS02AA07,QS03AA01,R02AB01,S01AA03,S02AA07,S03AA01"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neom,neomyc"	"NA"	5	"g"	1	"g"	"10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
 "NET"	441306	"Netilmicin"	"Aminoglycosides"	"J01GB07,QJ01GB07,QS01AA23,S01AA23"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neti,netilm"	"netillin,netilmicina,netilmicine,netilmicinum,netilyn,netira,netromicine,netromycin,nettacin,ntromicine,ntromycin,vectacin,zetamicin"	0.35	"g"	0.35	"g"	"18954-8,25263-5,358-2,359-0,360-8,361-6,3848-9,3849-7,3850-5,47385-0,59565-2,59566-0,59567-8,7035-9"
-"NIC"	9507	"Nicarbazin"	"Other antibacterials"	"NA"			"NA"	"nicarb,nicarbasin,nicarbazine,nicarmix,nicoxin,nicrazin,nicrazine,nirazin"					"NA"
-"NIF"	71946	"Nifuroquine"	"Fluoroquinolones"	"NA"			"NA"	"abimasten,nifuroquina,nifuroquinum,quinaldofur"					"NA"
-"NFR"	9571062	"Nifurtoinol"	"Other antibacterials"	"J01XE02,QJ01XE02"	"Other antibacterials"	"Nitrofuran derivatives"	"NA"	"levantin,nifurmazol,nifurmazole,nifurmazolo,nifurmazolum,nifurtoinolo,nifurtoinolum,urfadin,urfadine,urfadyn"	0.16	"g"			"NA"
-"NTZ"	41684	"Nitazoxanide"	"Other antibacterials"	"P01AX11"			"NA"	"alinia,benzamide,colufase,cryptaz,daxon,dexidex,heliton,kidonax,nitax,nitaxozanid,nitaxozanide,nitazox,nitazoxamide,nitazoxanid,nitazoxanida,nitazoxanidum,nitrazoxanide,pacovanton,paramix,phavic"	1	"g"			"73595-1,73617-3,73640-5"
-"NIT"	6604200	"Nitrofurantoin"	"Other antibacterials"	"J01XE01,QJ01XE01"	"Other antibacterials"	"Nitrofuran derivatives"	"f,f/m,fd,ft,ni,nit,nit16,nitr,nitro"	"alfuran,benkfuran,berkfuran,berkfurin,ceduran,chemiofuran,cistofuran,cyantin,cystit,dantafur,fuamed,furabid,furachel,furadantin,furadantine,furadantoin,furadoin,furadoine,furadonin,furadonine,furadoninum,furadontin,furalan,furaloid,furantoina,furatoin,furedan,furina,furobactina,furodantin,gerofuran,ituran,macpac,macrobid,macrodantin,macrodantina,macrofuran,macrofurin,nierofu,nifuraden,nifuradene,nifuradeno,nifuradenum,nifuradine,nifurantin,nifuretten,nitoin,nitrex,nitrofuradantin,nitrofurantoina,nitrofurantoine,nitrofurantoinum,novofuran,orafuran,oxafuradene,oxafurandene,oxifuradene,oxyfuradene,parfuran,phenurin,renafur,siraliden,trantoin,uerineks,urizept,urodin,urofuran,urofurin,urolisa,urolong,uvamin,welfurin,zoofurin"	0.2	"g"			"18955-5,362-4,363-2,364-0,365-7,3860-4,7036-7"
-"NIZ"	5447130	"Nitrofurazone"	"Other antibacterials"	"NA"			"nitfur"	"acutol,aldomycin,alfucin,amifur,babrocid,becafurazone,biofuracina,biofurea,chemofuran,chixin,cocafurin,coxistat,dermofural,dymazone,dynazone,eldezol,fedacin,flavazone,fracine,furacilin,furacilinum,furacillin,furacin,furacine,furacinetten,furacoccid,furacort,furacycline,furaderm,furagent,furalcyn,furaldon,furalone,furametral,furaplast,furaseptyl,furaskin,furatsilin,furaziline,furazin,furazina,furazyme,furesol,furosem,fuvacillin,hemofuran,hydrazinecarboxamide,ibiofural,mammex,mastofuran,monafuracin,monafuracis,monofuracin,nefco,nifucin,nifurid,nifuzon,nitrofural,nitrofuralum,nitrofuran,nitrofurane,nitrofurazan,nitrofurazonum,nitrofurol,nitrozone,otofural,otofuran,rivafurazon,rivopon,sanfuran,semioxamazide,vabrocid,vadrocid,yatrocin"					"20388-5,87793-6"
-"NTR"	19910	"Nitroxoline"	"Fluoroquinolones"	"J01XX07,QJ01XX07"	"Other antibacterials"	"Other antibacterials"	"NA"	"galinok,isinok,nibiol,nicene,nitroxlina,nitroxolin,nitroxolina,nitroxolinum,noxibiol,noxin"	1	"g"			"25608-1,25723-8,32382-4,54181-3,55688-6"
-"NOR"	4539	"Norfloxacin"	"Fluoroquinolones"	"J01MA06,QJ01MA06,QS01AE02,S01AE02"	"Quinolone antibacterials"	"Fluoroquinolones"	"nor,norf,norflo,nx,nxn"	"baccidal,barazan,chibroxin,chibroxine,chibroxol,fulgram,gonorcin,lexinor,nolicin,noracin,noraxin,norflo,norfloxacine,norfloxacino,norfloxacinum,norocin,noroxin,noroxine,norxacin,sebercim,uroxacin,utinor,zoroxin"	0.8	"g"			"18956-3,366-5,367-3,368-1,369-9,3867-9,41504-2,7037-5"
-"NOR-S"		"Norfloxacin screening test"	"Fluoroquinolones"	"NA"			"nor screen"	"NA"					"NA"
-"NME"		"Norfloxacin/metronidazole"	"Fluoroquinolones"	"J01RA14,QJ01RA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"NTI"		"Norfloxacin/tinidazole"	"Fluoroquinolones"	"J01RA13,QJ01RA13"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"NIC"	9507	"Nicarbazin"	"Other"	"NA"			"NA"	"nicarb,nicarbasin,nicarbazine,nicarmix,nicoxin,nicrazin,nicrazine,nirazin"					"NA"
+"NIF"	71946	"Nifuroquine"	"Fluoroquinolones,Quinolones"	"NA"			"NA"	"abimasten,nifuroquina,nifuroquinum,quinaldofur"					"NA"
+"NFR"	9571062	"Nifurtoinol"	"Nitrofurans"	"J01XE02,QJ01XE02"	"Other antibacterials"	"Nitrofuran derivatives"	"NA"	"levantin,nifurmazol,nifurmazole,nifurmazolo,nifurmazolum,nifurtoinolo,nifurtoinolum,urfadin,urfadine,urfadyn"	0.16	"g"			"NA"
+"NTZ"	41684	"Nitazoxanide"	"Other"	"P01AX11"			"NA"	"alinia,benzamide,colufase,cryptaz,daxon,dexidex,heliton,kidonax,nitax,nitaxozanid,nitaxozanide,nitazox,nitazoxamide,nitazoxanid,nitazoxanida,nitazoxanidum,nitrazoxanide,pacovanton,paramix,phavic"	1	"g"			"73595-1,73617-3,73640-5"
+"NIT"	6604200	"Nitrofurantoin"	"Nitrofurans"	"J01XE01,QJ01XE01"	"Other antibacterials"	"Nitrofuran derivatives"	"f,f/m,fd,ft,ni,nit,nit16,nitr,nitro"	"alfuran,benkfuran,berkfuran,berkfurin,ceduran,chemiofuran,cistofuran,cyantin,cystit,dantafur,fuamed,furabid,furachel,furadantin,furadantine,furadantoin,furadoin,furadoine,furadonin,furadonine,furadoninum,furadontin,furalan,furaloid,furantoina,furatoin,furedan,furina,furobactina,furodantin,gerofuran,ituran,macpac,macrobid,macrodantin,macrodantina,macrofuran,macrofurin,nierofu,nifuraden,nifuradene,nifuradeno,nifuradenum,nifuradine,nifurantin,nifuretten,nitoin,nitrex,nitrofuradantin,nitrofurantoina,nitrofurantoine,nitrofurantoinum,novofuran,orafuran,oxafuradene,oxafurandene,oxifuradene,oxyfuradene,parfuran,phenurin,renafur,siraliden,trantoin,uerineks,urizept,urodin,urofuran,urofurin,urolisa,urolong,uvamin,welfurin,zoofurin"	0.2	"g"			"18955-5,362-4,363-2,364-0,365-7,3860-4,7036-7"
+"NIZ"	5447130	"Nitrofurazone"	"Nitrofurans"	"NA"			"nitfur"	"acutol,aldomycin,alfucin,amifur,babrocid,becafurazone,biofuracina,biofurea,chemofuran,chixin,cocafurin,coxistat,dermofural,dymazone,dynazone,eldezol,fedacin,flavazone,fracine,furacilin,furacilinum,furacillin,furacin,furacine,furacinetten,furacoccid,furacort,furacycline,furaderm,furagent,furalcyn,furaldon,furalone,furametral,furaplast,furaseptyl,furaskin,furatsilin,furaziline,furazin,furazina,furazyme,furesol,furosem,fuvacillin,hemofuran,hydrazinecarboxamide,ibiofural,mammex,mastofuran,monafuracin,monafuracis,monofuracin,nefco,nifucin,nifurid,nifuzon,nitrofural,nitrofuralum,nitrofuran,nitrofurane,nitrofurazan,nitrofurazonum,nitrofurol,nitrozone,otofural,otofuran,rivafurazon,rivopon,sanfuran,semioxamazide,vabrocid,vadrocid,yatrocin"					"20388-5,87793-6"
+"NTR"	19910	"Nitroxoline"	"Fluoroquinolones,Quinolones"	"J01XX07,QJ01XX07"	"Other antibacterials"	"Other antibacterials"	"NA"	"galinok,isinok,nibiol,nicene,nitroxlina,nitroxolin,nitroxolina,nitroxolinum,noxibiol,noxin"	1	"g"			"25608-1,25723-8,32382-4,54181-3,55688-6"
+"NOR"	4539	"Norfloxacin"	"Fluoroquinolones,Quinolones"	"J01MA06,QJ01MA06,QS01AE02,S01AE02"	"Quinolone antibacterials"	"Fluoroquinolones"	"nor,norf,norflo,nx,nxn"	"baccidal,barazan,chibroxin,chibroxine,chibroxol,fulgram,gonorcin,lexinor,nolicin,noracin,noraxin,norflo,norfloxacine,norfloxacino,norfloxacinum,norocin,noroxin,noroxine,norxacin,sebercim,uroxacin,utinor,zoroxin"	0.8	"g"			"18956-3,366-5,367-3,368-1,369-9,3867-9,41504-2,7037-5"
+"NOR-S"		"Norfloxacin screening test"	"Fluoroquinolones,Quinolones"	"NA"			"nor screen"	"NA"					"NA"
+"NME"		"Norfloxacin/metronidazole"	"Fluoroquinolones,Quinolones"	"J01RA14,QJ01RA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"NTI"		"Norfloxacin/tinidazole"	"Fluoroquinolones,Quinolones"	"J01RA13,QJ01RA13"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
 "NVA"	10419027	"Norvancomycin"	"Glycopeptides"	"NA"			"NA"	"NA"					"NA"
-"NOV"	54675769	"Novobiocin"	"Other antibacterials"	"QJ01XX95"			"novo,novobi"	"albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
-"NYS"	6433272	"Nystatin"	"Antifungals/antimycotics"	"A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01"			"nyst,nystan"	"biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex"	1.5	"MU"			"10697-1,10698-9,18958-9,35824-2,55689-4"
-"OFX"	4583	"Ofloxacin"	"Fluoroquinolones"	"J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16"	"Quinolone antibacterials"	"Fluoroquinolones"	"of,ofl,oflo,ofloxa,ofx"	"exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,visiren,zanocin"	0.4	"g"	0.4	"g"	"18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8"
-"OOR"		"Ofloxacin/ornidazole"	"Fluoroquinolones"	"J01RA09,QJ01RA09"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"OLE"	72493	"Oleandomycin"	"Macrolides/lincosamides"	"J01FA05,QJ01FA05"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"oleand"	"amimycin,landomycin,matromycin,oleandomicina,oleandomycine,oleandomycinum,romicil"	1	"g"			"18960-5,378-0,379-8,380-6,381-4,55690-2"
+"NOV"	54675769	"Novobiocin"	"Other"	"QJ01XX95"			"novo,novobi"	"albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
+"NYS"	6433272	"Nystatin"	"Antifungals"	"A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01"			"nyst,nystan"	"biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex"	1.5	"MU"			"10697-1,10698-9,18958-9,35824-2,55689-4"
+"OFX"	4583	"Ofloxacin"	"Fluoroquinolones,Quinolones"	"J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16"	"Quinolone antibacterials"	"Fluoroquinolones"	"of,ofl,oflo,ofloxa,ofx"	"exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,visiren,zanocin"	0.4	"g"	0.4	"g"	"18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8"
+"OOR"		"Ofloxacin/ornidazole"	"Fluoroquinolones,Quinolones"	"J01RA09,QJ01RA09"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"OLE"	72493	"Oleandomycin"	"Macrolides"	"J01FA05,QJ01FA05"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"oleand"	"amimycin,landomycin,matromycin,oleandomicina,oleandomycine,oleandomycinum,romicil"	1	"g"			"18960-5,378-0,379-8,380-6,381-4,55690-2"
 "OMC"	54697325	"Omadacycline"	"Tetracyclines"	"J01AA15,QJ01AA15"			"NA"	"amadacycline"	0.3	"g"	0.1	"g"	"73594-4,73616-5,73639-7"
-"OPT"	87880	"Optochin"	"Other antibacterials"	"NA"			"NA"	"aflukin,auriquin,biquinate,chinidin,chinidine,chinimetten,chinin,chinine,conchinin,conchinine,conquinine,dentojel,dihydrochinidin,dihydroquinidine,dihydroquinine,hydroconchinine,hydroconquinine,hydroquinidine,kinidin,numoquin,optochine,optoquine,pitayine,qualaquin,quinaglute,quinicardine,quinidex,quinidine,quiniduran,quinindine,quinine,quinineanhydrous,quinora,quinsan,rezquin"					"100055-3,73665-2"
-"ORB"	60605	"Orbifloxacin"	"Fluoroquinolones"	"QJ01MA95"			"orbifl"	"orbax"					"35825-9,35826-7,35827-5"
-"ORI"	16136912	"Oritavancin"	"Glycopeptides"	"J01XA05,QJ01XA05"	"Other antibacterials"	"Glycopeptide antibacterials"	"orit,oritav"	"NA"					"41707-1,41708-9,41709-7,41736-0"
-"ORS"		"Ormetroprim/sulfamethoxazole"	"Other antibacterials"	"NA"			"NA"	"NA"					"73593-6,73615-7,73638-9"
-"ORN"	28061	"Ornidazole"	"Other antibacterials"	"G01AF06,J01XD03,P01AB03,QG01AF06,QJ01XD03,QP51AA03"	"Other antibacterials"	"Imidazole derivatives"	"NA"	"levornidazole,madelen,ornidal,ornidazolum,tiberal"	1.5	"g"	1	"g"	"55691-0,55692-8,55693-6,55694-4"
-"OTE"	77050711	"Oteseconazole"	"Antifungals/antimycotics"	"J02AC06,QJ02AC06"	"Antimycotics for systemic use"	"Triazole derivatives"	"NA"	"quilseconazole,vivijoa"	21	"mg"			"NA"
-"OXA"	6196	"Oxacillin"	"Beta-lactams/penicillins"	"J01CF04,QJ01CF04,QJ51CF04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"ox,oxa,oxac,oxacil,oxal,oxs"	"bactocill,bristopen,cryptocillin,micropenin,ossacillina,oxabel,oxabelsalt,oxacilina,oxacillinanhydrous,oxacilline,oxacillinhydrate,oxacillinsalt,oxacillinum,oxazocillin,oxazocilline,penstapho,prostaphlin,prostaphlyn,resistopen,stapenor"	2	"g"	2	"g"	"18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1"
-"OXA-S"		"Oxacillin screening test"	"Beta-lactams/penicillins"	"NA"			"oxa screen"	"NA"					"NA"
+"OPT"	87880	"Optochin"	"Other"	"NA"			"NA"	"aflukin,auriquin,biquinate,chinidin,chinidine,chinimetten,chinin,chinine,conchinin,conchinine,conquinine,dentojel,dihydrochinidin,dihydroquinidine,dihydroquinine,hydroconchinine,hydroconquinine,hydroquinidine,kinidin,numoquin,optochine,optoquine,pitayine,qualaquin,quinaglute,quinicardine,quinidex,quinidine,quiniduran,quinindine,quinine,quinineanhydrous,quinora,quinsan,rezquin"					"100055-3,73665-2"
+"ORB"	60605	"Orbifloxacin"	"Fluoroquinolones,Quinolones"	"QJ01MA95"			"orbifl"	"orbax"					"35825-9,35826-7,35827-5"
+"ORI"	16136912	"Oritavancin"	"Lipoglycopeptides,Glycopeptides"	"J01XA05,QJ01XA05"	"Other antibacterials"	"Glycopeptide antibacterials"	"orit,oritav"	"NA"					"41707-1,41708-9,41709-7,41736-0"
+"ORS"		"Ormetroprim/sulfamethoxazole"	"Trimethoprims,Sulfonamides"	"NA"			"NA"	"NA"					"73593-6,73615-7,73638-9"
+"ORN"	28061	"Ornidazole"	"Other"	"G01AF06,J01XD03,P01AB03,QG01AF06,QJ01XD03,QP51AA03"	"Other antibacterials"	"Imidazole derivatives"	"NA"	"levornidazole,madelen,ornidal,ornidazolum,tiberal"	1.5	"g"	1	"g"	"55691-0,55692-8,55693-6,55694-4"
+"OTE"	77050711	"Oteseconazole"	"Antifungals"	"J02AC06,QJ02AC06"	"Antimycotics for systemic use"	"Triazole derivatives"	"NA"	"quilseconazole,vivijoa"	21	"mg"			"NA"
+"OXA"	6196	"Oxacillin"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"J01CF04,QJ01CF04,QJ51CF04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"ox,oxa,oxac,oxacil,oxal,oxs"	"bactocill,bristopen,cryptocillin,micropenin,ossacillina,oxabel,oxabelsalt,oxacilina,oxacillinanhydrous,oxacilline,oxacillinhydrate,oxacillinsalt,oxacillinum,oxazocillin,oxazocilline,penstapho,prostaphlin,prostaphlyn,resistopen,stapenor"	2	"g"	2	"g"	"18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1"
+"OXA-S"		"Oxacillin screening test"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"NA"			"oxa screen"	"NA"					"NA"
 "OXO"	4628	"Oxolinic acid"	"Quinolones"	"J01MB05,QJ01MB05"	"Quinolone antibacterials"	"Other quinolones"	"oxoaci"	"aqualinic,cistopax,dioxacin,emyrenil,gramurin,inoxyl,nidantin,oksaren,orthurine,ossian,oxoboi,oxolinic,pietil,prodoxal,prodoxol,starner,tiurasin,ultibid,urinox,uritrate,urotrate,uroxol,utibid"	1	"g"			"NA"
 "OXY"	54675779	"Oxytetracycline"	"Tetracyclines"	"A01AB25,D06AA03,G01AA07,J01AA06,QA01AB25,QD06AA03,QG01AA07,QG51AA01,QJ01AA06,QJ51AA06,QS01AA04,S01AA04"	"Tetracyclines"	"Tetracyclines"	"oxytet"	"achromycin,actisite,adamycin,artomycin,berkmycen,biostat,bristacycline,cancycline,cyclopar,dabicycline,diacycine,dumocyclin,embryostat,fanterrin,galsenomycin,geomycin,geotilin,hostacycline,hydroxytetracyclinum,lenocycline,macocyn,medamycin,mephacyclin,nitox,oksisyklin,ossitetraciclina,oxitetraciclina,oxitetracyclin,oxitetracycline,oxitetracyclinum,oxymycin,oxypam,oxyterracin,oxyterracine,oxyterracyne,oxytetracid,oxytetracyclin,oxytetracyclinum,paltet,partrex,pennox,piracaps,proteroxyna,qidtet,quadracycline,quatrex,remicyclin,retet,ricycline,riomitsin,ryomycin,solkaciclina,stevacin,stilciclina,subamycin,sumycin,supramycin,sustamycin,tarocyn,tarosin,tefilin,teline,telotrex,teravit,terrafungine,terramitsin,terramycine,tetrabakat,tetrabid,tetrablet,tetracaps,tetracompren,tetrakap,tetralution,tetramavan,tetramed,tetran,tetrosol,topicycline,triphacyclin,unicin,ursocyclin,ursocycline,vetquamycin"	1	"g"	1	"g"	"17396-3,18962-1,25266-8,386-3,387-1,388-9,389-7,55699-3,87595-5"
-"OZN"		"Ozenoxacin"		"D06AX14,QD06AX14"			"NA"	"NA"					"NA"
+"OZN"		"Ozenoxacin"	"Quinolones"	"D06AX14,QD06AX14"			"NA"	"NA"					"NA"
 "PAS"	4649	"P-aminosalicylic acid"	"Antimycobacterials"	"NA"			"pasraa"	"NA"					"NA"
-"PAN"	72015	"Panipenem"	"Carbapenems"	"NA"			"NA"	"carbenin,panipenemum,penipanem"					"100056-1,53823-1"
-"PAR"	165580	"Paromomycin"	"Other antibacterials"	"A07AA06,QA07AA06,QJ01GB92"			"NA"	"aminosidin,amminosidin,crestomycin,estomycin,gabbromycin,gabromycin,humatin,humycin,hydroxymycin,monomycin,paramomycin,paromomicina,paromomycine,paromomycinum,paucimycin,paucimycinum"	3	"g"			"51719-3,53824-9,55700-9,55701-7,55702-5"
-"PAZ"	65957	"Pazufloxacin"	"Fluoroquinolones"	"J01MA18,QJ01MA18"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"pazufloxacine,pazufloxacino,pazufloxacinum"			1	"g"	"NA"
-"PEF"	51081	"Pefloxacin"	"Fluoroquinolones"	"J01MA03,QJ01MA03"	"Quinolone antibacterials"	"Fluoroquinolones"	"pefl,perflo"	"labocton,pefbid,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,pefocin,pefran,pelox"	0.8	"g"	0.8	"g"	"18963-9,35828-3,390-5,3906-5,7040-9"
-"PEF-S"		"Pefloxacin screening test"	"Fluoroquinolones"	"NA"			"pef screen"	"NA"					"NA"
-"PNM"	10250769	"Penamecillin"	"Beta-lactams/penicillins"	"J01CE06,QJ01CE06"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"havapen,hydroxymethyl,penamecilina,penamecillina,penamecilline,penamecillinum"	1.05	"g"			"NA"
-"PNO"		"Penicillin/novobiocin"	"Beta-lactams/penicillins"	"NA"			"pennov"	"NA"					"35872-1,35873-9,35874-7"
-"PSU"		"Penicillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			"NA"	"NA"					"NA"
+"PAN"	72015	"Panipenem"	"Carbapenems,Beta-lactams"	"NA"			"NA"	"carbenin,panipenemum,penipanem"					"100056-1,53823-1"
+"PAR"	165580	"Paromomycin"	"Other"	"A07AA06,QA07AA06,QJ01GB92"			"NA"	"aminosidin,amminosidin,crestomycin,estomycin,gabbromycin,gabromycin,humatin,humycin,hydroxymycin,monomycin,paramomycin,paromomicina,paromomycine,paromomycinum,paucimycin,paucimycinum"	3	"g"			"51719-3,53824-9,55700-9,55701-7,55702-5"
+"PAZ"	65957	"Pazufloxacin"	"Fluoroquinolones,Quinolones"	"J01MA18,QJ01MA18"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"pazufloxacine,pazufloxacino,pazufloxacinum"			1	"g"	"NA"
+"PEF"	51081	"Pefloxacin"	"Fluoroquinolones,Quinolones"	"J01MA03,QJ01MA03"	"Quinolone antibacterials"	"Fluoroquinolones"	"pefl,perflo"	"labocton,pefbid,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,pefocin,pefran,pelox"	0.8	"g"	0.8	"g"	"18963-9,35828-3,390-5,3906-5,7040-9"
+"PEF-S"		"Pefloxacin screening test"	"Fluoroquinolones,Quinolones"	"NA"			"pef screen"	"NA"					"NA"
+"PNM"	10250769	"Penamecillin"	"Penicillins,Beta-lactams"	"J01CE06,QJ01CE06"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"havapen,hydroxymethyl,penamecilina,penamecillina,penamecilline,penamecillinum"	1.05	"g"			"NA"
+"PNO"		"Penicillin/novobiocin"	"Penicillins,Beta-lactams"	"NA"			"pennov"	"NA"					"35872-1,35873-9,35874-7"
+"PSU"		"Penicillin/sulbactam"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"NA"	"NA"					"NA"
 "PNM1"	54686187	"Penimepicycline"	"Tetracyclines"	"J01AA10,QJ01AA10"	"Tetracyclines"	"Tetracyclines"	"NA"	"criseocil,duamine,geotricyn,hydrocycline,penetracyne,penimepiciclina,penimepicyclinum"					"NA"
 "PIM"	65453	"Pentisomicin"	"Aminoglycosides"	"NA"			"NA"	"mutamicin,mutamycin,pentisomicina,pentisomicine,pentisomicinum"					"NA"
-"PTZ"	55250256	"Pentizidone"	"Other antibacterials"	"NA"			"NA"	"pentizidona,pentizidonum"					"NA"
-"PEX"	16132253	"Pexiganan"	"Other antibacterials"	"NA"			"NA"	"cytolex,mangainin"					"NA"
-"PHE"	272833	"Pheneticillin"	"Beta-lactams/penicillins"	"J01CE05,QJ01CE05"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"fene"	"alfacillin,alticina,antibiocin,arcacil,arcasin,astracillin,bendralan,beromycin,brocsil,broxil,chemipen,cliacil,darcil,feneticilina,feneticillin,feneticillina,feneticilline,fenocin,icipen,isocillin,ispenoral,kavepenin,maxipen,optipen,oralopen,orapen,ospeneff,pedipen,penagen,pencompren,penemve,peniplus,penova,pensig,penvikal,phenethicilin,phenethicillin,phenethicillinum,pheneticilline,pheneticillinum,primcillin,priospen,roscopenin,semopen,suspen,synapen,syncillin,synerpenin,synthecillin,synthecilline,synthepen,triospen,vamosyn,veetids,vepen"	1	"g"			"NA"
-"PHN"	6869	"Phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"J01CE02,QJ01CE02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"fepe,peni v,penicillin v,phepen,pnv,pv"	"apopen,calcipen,fenacilin,fenospen,meropenin,oracillin,oracilline,oratren,orocillin,ospen,phenocillin,phenomycilline,phenopenicillin,rocilin,stabicillin,vebecillin"	2	"g"			"NA"
-"PMR"	5284447	"Pimaricin"	"Antifungals/antimycotics"	"NA"			"natamycin"	"delvocid,delvolan,delvopos,mycophyt,myprozine,natacyn,natafucin,natajen,natamatrix,natamax,natamicina,natamycin,natamycine,natamycinum,pimafucin,pimaracin,pimaricine,pimarizin,synogil,tennecetin"					"NA"
+"PTZ"	55250256	"Pentizidone"	"Other"	"NA"			"NA"	"pentizidona,pentizidonum"					"NA"
+"PEX"	16132253	"Pexiganan"	"Other"	"NA"			"NA"	"cytolex,mangainin"					"NA"
+"PHE"	272833	"Pheneticillin"	"Penicillins,Beta-lactams"	"J01CE05,QJ01CE05"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"fene"	"alfacillin,alticina,antibiocin,arcacil,arcasin,astracillin,bendralan,beromycin,brocsil,broxil,chemipen,cliacil,darcil,feneticilina,feneticillin,feneticillina,feneticilline,fenocin,icipen,isocillin,ispenoral,kavepenin,maxipen,optipen,oralopen,orapen,ospeneff,pedipen,penagen,pencompren,penemve,peniplus,penova,pensig,penvikal,phenethicilin,phenethicillin,phenethicillinum,pheneticilline,pheneticillinum,primcillin,priospen,roscopenin,semopen,suspen,synapen,syncillin,synerpenin,synthecillin,synthecilline,synthepen,triospen,vamosyn,veetids,vepen"	1	"g"			"NA"
+"PHN"	6869	"Phenoxymethylpenicillin"	"Penicillins,Beta-lactams"	"J01CE02,QJ01CE02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"fepe,peni v,penicillin v,phepen,pnv,pv"	"apopen,calcipen,fenacilin,fenospen,meropenin,oracillin,oracilline,oratren,orocillin,ospen,phenocillin,phenomycilline,phenopenicillin,rocilin,stabicillin,vebecillin"	2	"g"			"NA"
+"PMR"	5284447	"Pimaricin"	"Antifungals"	"NA"			"natamycin"	"delvocid,delvolan,delvopos,mycophyt,myprozine,natacyn,natafucin,natajen,natamatrix,natamax,natamicina,natamycin,natamycine,natamycinum,pimafucin,pimaracin,pimaricine,pimarizin,synogil,tennecetin"					"NA"
 "PPA"	4831	"Pipemidic acid"	"Quinolones"	"J01MB04,QJ01MB04"	"Quinolone antibacterials"	"Other quinolones"	"pipaci,pipz,pizu"	"deblaston,dolcol,filtrax,karunomazin,memento,nuril,palin,pipedac,pipemid,pipemidate,pipemidic,pipemidicacid,pipram,pipurin,tractur,uromidin,urosten,uroval"	0.8	"g"			"NA"
-"PIP"	43672	"Piperacillin"	"Beta-lactams/penicillins"	"J01CA12,QJ01CA12"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"pi,pip,pipc,pipe,pipera,pp"	"penmalin,pentcillin,peperacillin,peracin,piperacilina,piperacillina,piperacilline,piperacillinhydrate,piperacillinum,pipercillin,pipracil,tazocin"			14	"g"	"101490-1,101491-9,18969-6,18970-4,25268-4,3972-7,407-7,408-5,409-3,410-1,411-9,412-7,413-5,414-3,54197-9,54198-7,54199-5,55704-1,7043-3,7044-1"
-"PIS"		"Piperacillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR05,QJ01CR05"			"NA"	"NA"			14	"g"	"54197-9,54198-7,54199-5,55704-1"
-"TZP"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"J01CR05,QJ01CR05"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp"	"piptazobactam,tazonam,zobactin,zosyn"			14	"g"	"101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1"
-"PRC"	71978	"Piridicillin"	"Beta-lactams/penicillins"	"NA"			"NA"	"NA"					"NA"
-"PRL"	157385	"Pirlimycin"	"Macrolides/lincosamides"	"QJ51FF90"			"pirlim"	"pirlimycina,pirlimycine,pirlimycinum,pirsue"					"35829-1,35830-9,35831-7"
+"PIP"	43672	"Piperacillin"	"Ureidopenicillins,Penicillins,Beta-lactams"	"J01CA12,QJ01CA12"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"pi,pip,pipc,pipe,pipera,pp"	"penmalin,pentcillin,peperacillin,peracin,piperacilina,piperacillina,piperacilline,piperacillinhydrate,piperacillinum,pipercillin,pipracil,tazocin"			14	"g"	"101490-1,101491-9,18969-6,18970-4,25268-4,3972-7,407-7,408-5,409-3,410-1,411-9,412-7,413-5,414-3,54197-9,54198-7,54199-5,55704-1,7043-3,7044-1"
+"PIS"		"Piperacillin/sulbactam"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"NA"	"NA"			14	"g"	"54197-9,54198-7,54199-5,55704-1"
+"TZP"	461573	"Piperacillin/tazobactam"	"Ureidopenicillins,Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"J01CR05,QJ01CR05"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp"	"piptazobactam,tazonam,zobactin,zosyn"			14	"g"	"101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1"
+"PRC"	71978	"Piridicillin"	"Penicillins,Beta-lactams"	"NA"			"NA"	"NA"					"NA"
+"PRL"	157385	"Pirlimycin"	"Lincosamides,Macrolides"	"QJ51FF90"			"pirlim"	"pirlimycina,pirlimycine,pirlimycinum,pirsue"					"35829-1,35830-9,35831-7"
 "PIR"	4855	"Piromidic acid"	"Quinolones"	"J01MB03,QJ01MB03"	"Quinolone antibacterials"	"Other quinolones"	"NA"	"bactramyl,enterol,gastrurol,panacid,pirodal,piromidate,reelon,septural,urisept,uropir,zaomeal"	2	"g"			"NA"
-"PVM"	33478	"Pivampicillin"	"Beta-lactams/penicillins"	"J01CA02,QJ01CA02"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"pivaloylampicillin,pivampicilina,pivampicilline,pivampicillinum"	1.05	"g"			"18971-2,415-0,416-8,417-6,418-4"
-"PME"	115163	"Pivmecillinam"	"Beta-lactams/penicillins"	"J01CA08,QJ01CA08"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"pivmec"	"coactabs,melysin,pivamdinocillin,pivmecilinamo,pivmecillinamum,selexid"	0.6	"g"			"NA"
+"PVM"	33478	"Pivampicillin"	"Penicillins,Beta-lactams"	"J01CA02,QJ01CA02"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"pivaloylampicillin,pivampicilina,pivampicilline,pivampicillinum"	1.05	"g"			"18971-2,415-0,416-8,417-6,418-4"
+"PME"	115163	"Pivmecillinam"	"Penicillins,Beta-lactams"	"J01CA08,QJ01CA08"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"pivmec"	"coactabs,melysin,pivamdinocillin,pivmecilinamo,pivmecillinamum,selexid"	0.6	"g"			"NA"
 "PLZ"	42613186	"Plazomicin"	"Aminoglycosides"	"J01GB14,QJ01GB14"			"NA"	"zemdri"					"73592-8,73614-0,73637-1,92024-9,94719-2"
 "PLB"	49800004	"Polymyxin B"	"Polymyxins"	"A07AA05,J01XB02,QA07AA05,QJ01XB02,QJ51XB02,QS01AA18,QS02AA11,QS03AA03,S01AA18,S02AA11,S03AA03"	"Other antibacterials"	"Polymyxins"	"pb,pol,polb,poly,poly b,polyb,polymixin,polymixin b"	"aerosporin"	3	"MU"	0.15	"g"	"17473-0,18972-0,25269-2,35832-5,419-2,420-0,421-8,422-6"
 "POP"		"Polymyxin B/polysorbate 80"	"Polymyxins"	"NA"			"NA"	"NA"					"NA"
-"POS"	468595	"Posaconazole"	"Antifungals/antimycotics"	"J02AC04,QJ02AC04"	"Antimycotics for systemic use"	"Triazole derivatives"	"posa,posaco"	"noxafil,schering,spriafil"	0.3	"g"	0.3	"g"	"53731-6,54186-2,54187-0,54188-8,54189-6,80545-7"
-"PRA"	9802884	"Pradofloxacin"	"Fluoroquinolones"	"QJ01MA97"			"NA"	"pudofloxacin,veraflox"					"76148-6,87800-9"
-"PRX"	71455	"Premafloxacin"	"Fluoroquinolones"	"NA"			"premaf"	"premafloxacine,premafloxacino"					"73591-0,73613-2,73636-3"
+"POS"	468595	"Posaconazole"	"Antifungals"	"J02AC04,QJ02AC04"	"Antimycotics for systemic use"	"Triazole derivatives"	"posa,posaco"	"noxafil,schering,spriafil"	0.3	"g"	0.3	"g"	"53731-6,54186-2,54187-0,54188-8,54189-6,80545-7"
+"PRA"	9802884	"Pradofloxacin"	"Fluoroquinolones,Quinolones"	"QJ01MA97"			"NA"	"pudofloxacin,veraflox"					"76148-6,87800-9"
+"PRX"	71455	"Premafloxacin"	"Fluoroquinolones,Quinolones"	"NA"			"premaf"	"premafloxacine,premafloxacino"					"73591-0,73613-2,73636-3"
 "PMD"	456199	"Pretomanid"	"Antimycobacterials"	"J04AK08,QJ04AK08"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"NA"	"NA"	0.2	"g"			"93850-6"
-"PRM"	6446787	"Primycin"	"Macrolides/lincosamides"	"NA"			"NA"	"chinopricin,debrycin,primicina,primycine"					"NA"
-"PRI"	11979535	"Pristinamycin"	"Macrolides/lincosamides"	"J01FG01,QJ01FG01"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"pris,pristi"	"eskalin,micamicina,mikamycin,mikamycine,mikamycinum,ostreogricina,ostreogrycin,ostreogrycine,ostreogrycinum,pristinamicina,pristinamycine,pristinamycinum,pyostacine,stafac,stafytracine,stajac,staphylomycin,stapyocine,starfac,virgimycin,virgimycine,virginiamicina,virginiamycin,virginiamycina,virginiamycinum"	2	"g"			"32383-2,35833-3,35834-1,55709-0"
-"PRB"	5903	"Procaine benzylpenicillin"	"Beta-lactams/penicillins"	"J01CE09,QJ01CE09,QJ51CE09"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"afsillin,aquacilina,aquacillin,aquasuspen,avloprocil,cilicaine,crysticillin,depocillin,despacilina,distaquaine,duphapen,duracillin,hostacillin,hydracillin,kabipenin,ledercillin,millicillin,mylipen,neoproc,nopcaine,parencillin,premocillin,procanodia,prostabillin,retardillin,sharcillin,vetspen,vitablend,wycillin"			0.6	"g"	"NA"
-"PRP"	92879	"Propicillin"	"Beta-lactams/penicillins"	"J01CE03,QJ01CE03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"baycillin,propicilina,propicilline,propicillinum"	0.9	"g"			"NA"
+"PRM"	6446787	"Primycin"	"Macrolides"	"NA"			"NA"	"chinopricin,debrycin,primicina,primycine"					"NA"
+"PRI"	11979535	"Pristinamycin"	"Streptogramins"	"J01FG01,QJ01FG01"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"pris,pristi"	"eskalin,micamicina,mikamycin,mikamycine,mikamycinum,ostreogricina,ostreogrycin,ostreogrycine,ostreogrycinum,pristinamicina,pristinamycine,pristinamycinum,pyostacine,stafac,stafytracine,stajac,staphylomycin,stapyocine,starfac,virgimycin,virgimycine,virginiamicina,virginiamycin,virginiamycina,virginiamycinum"	2	"g"			"32383-2,35833-3,35834-1,55709-0"
+"PRB"	5903	"Procaine benzylpenicillin"	"Penicillins,Beta-lactams"	"J01CE09,QJ01CE09,QJ51CE09"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"afsillin,aquacilina,aquacillin,aquasuspen,avloprocil,cilicaine,crysticillin,depocillin,despacilina,distaquaine,duphapen,duracillin,hostacillin,hydracillin,kabipenin,ledercillin,millicillin,mylipen,neoproc,nopcaine,parencillin,premocillin,procanodia,prostabillin,retardillin,sharcillin,vetspen,vitablend,wycillin"			0.6	"g"	"NA"
+"PRP"	92879	"Propicillin"	"Penicillins,Beta-lactams"	"J01CE03,QJ01CE03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"baycillin,propicilina,propicilline,propicillinum"	0.9	"g"			"NA"
 "PKA"	9872451	"Propikacin"	"Aminoglycosides"	"NA"			"NA"	"propikacina,propikacine,propikacinum"					"NA"
 "PTH"	666418	"Protionamide"	"Antimycobacterials"	"J04AD01,QJ04AD01"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"prot"	"ektebin,peteha,prothionamide,prothionamidum,protion,protionamid,protionamida,protionamidum,protionizina,tebeform,trevintix,tuberex"	0.75	"g"			"NA"
-"PRU"	65947	"Prulifloxacin"	"Fluoroquinolones"	"J01MA17,QJ01MA17"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"pruvel,quisnon,sword"	0.6	"g"			"100058-7,76145-2"
+"PRU"	65947	"Prulifloxacin"	"Fluoroquinolones,Quinolones"	"J01MA17,QJ01MA17"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"pruvel,quisnon,sword"	0.6	"g"			"100058-7,76145-2"
 "PZA"	1046	"Pyrazinamide"	"Antimycobacterials"	"J04AK01,QJ04AK01"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"pyra"	"aldinamid,aldinamide,eprazin,farmizina,isopas,novamid,pezetamid,piraldina,pirazimida,pirazinamid,pirazinamida,pirazinamide,pirazinecarboxamide,pyrafat,pyrazide,pyrazinamdie,pyrazinamidum,pyrazineamide,pyrizinamide,rifafour,rozide,tebrazid,tisamid,unipyranamide"	1.5	"g"			"11001-5,18973-8,20461-0,23632-3,25186-8,25229-6,25270-0,423-4,424-2,425-9,426-7,42935-7,55710-8,55711-6,56026-8,92242-7"
-"QDA"	11979418	"Quinupristin/dalfopristin"	"Macrolides/lincosamides"	"QJ01FG02"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"q/d,qda,qida,quda,rp,syn,synerc"	"synercid"					"23640-6,23641-4,33334-4,35835-8,58712-1"
-"RAC"	56052	"Ractopamine"	"Other antibacterials"	"NA"			"NA"	"bufenina,bufenine,buphenin,buphenine,bupheninum,luteonin,nilidrine,nylidrinum,optaflexx,paylean,prepar,ractopamina,ractopaminum,ritodrina,ritodrine,ritodrinium,tomax,utopar,yutopar"					"NA"
+"QDA"	11979418	"Quinupristin/dalfopristin"	"Streptogramins"	"QJ01FG02"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"q/d,qda,qida,quda,rp,syn,synerc"	"synercid"					"23640-6,23641-4,33334-4,35835-8,58712-1"
+"RAC"	56052	"Ractopamine"	"Other"	"NA"			"NA"	"bufenina,bufenine,buphenin,buphenine,bupheninum,luteonin,nilidrine,nylidrinum,optaflexx,paylean,prepar,ractopamina,ractopaminum,ritodrina,ritodrine,ritodrinium,tomax,utopar,yutopar"					"NA"
 "RAM"	16132338	"Ramoplanin"	"Glycopeptides"	"NA"			"ramopl"	"NA"					"41710-5,41711-3,41712-1,41737-8"
-"RZM"	10993211	"Razupenem"	"Carbapenems"	"NA"			"razupe"	"NA"					"73590-2,73612-4,73635-5"
-"RTP"	6918462	"Retapamulin"	"Other antibacterials"	"D06AX13,QD06AX13"	"Antibiotics for topical use"	"Other antibiotics for topical use"	"ret"	"altabax,altargo,rebapamulin,retapamulina"					"NA"
+"RZM"	10993211	"Razupenem"	"Carbapenems,Beta-lactams"	"NA"			"razupe"	"NA"					"73590-2,73612-4,73635-5"
+"RTP"	6918462	"Retapamulin"	"Other"	"D06AX13,QD06AX13"	"Antibiotics for topical use"	"Other antibiotics for topical use"	"ret"	"altabax,altargo,rebapamulin,retapamulina"					"NA"
 "RZF"		"Rezafungin"	"Antifungals"	"NA"			"NA"	"NA"					"NA"
-"RBC"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"L01EF02,QL01EF02"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"kisqali"	0.45	"g"			"NA"
+"RBC"	44631912	"Ribociclib"	"Antifungals"	"L01EF02,QL01EF02"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"kisqali"	0.45	"g"			"NA"
 "RST"	33042	"Ribostamycin"	"Aminoglycosides"	"J01GB10,QJ01GB10"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"NA"	"exaluren,hetangmycin,ribastamin,ribostamicina,ribostamycine,ribostamycinum,vistamycin,xylostatin"			1	"g"	"NA"
-"RID1"	16659285	"Ridinilazole"	"Other antibacterials"	"NA"			"NA"	"ridinilazol"					"NA"
-"RIB"	135398743	"Rifabutin"	"Antimycobacterials"	"J04AB04,QJ04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"ansamy,rifb"	"alfacid,ansamicin,ansamycins,ansatipin,ansatipine,assatipin,mycobutin,rifabutinum"	0.15	"g"			"100699-8,16100-0,16386-5,16387-3,19149-4,20386-9,23630-7,24032-5,25199-1,25200-7,25201-5,42655-1,42656-9,54183-9,96113-6"
-"RIF"	135398735	"Rifampicin"	"Antimycobacterials"	"J04AB02,QJ04AB02,QJ54AB02"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifa,rifamp"	"abrifam,archidyn,arficin,arzide,benemicin,doloresum,eremfat,famcin,fenampicin,rifadin,rifadine,rifagen,rifaldazin,rifaldazine,rifaldin,rifam,rifamor,rifampicina,rifampicine,rifampicinum,rifampin,rifamsolin,rifapiam,rifaprodin,rifcin,rifinah,rifobac,rifoldin,rifoldine,riforal,rimactan,rimactane,rimactazid,rimactizid,rimazid,sinerdol,tubocin"	0.6	"g"	0.6	"g"	"NA"
-"REI"	135483893	"Rifampicin/ethambutol/isoniazid"	"Antimycobacterials"	"J04AM07,QJ04AM07"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"isonarif,rifamate,rifamazid"					"NA"
-"RFI"		"Rifampicin/isoniazid"	"Antimycobacterials"	"J04AM02,QJ04AM02"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
-"RPEI"		"Rifampicin/pyrazinamide/ethambutol/isoniazid"	"Antimycobacterials"	"J04AM06,QJ04AM06"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
-"RPI"		"Rifampicin/pyrazinamide/isoniazid"	"Antimycobacterials"	"J04AM05,QJ04AM05"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
-"RFM"	6324616	"Rifamycin"	"Antimycobacterials"	"A07AA13,D06AX15,J04AB03,QA07AA13,QD06AX15,QJ04AB03,QJ54AB03,QS01AA16,QS02AA12,S01AA16,S02AA12"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifmyc"	"aemcolo,nacimycin,nancimycin,otofa,rifamastene,rifamicina,rifamycine,rifamycinum,rifocin,rifocyn,tuborin"	0.8	"g"	0.6	"g"	"NA"
-"RFP"	135403821	"Rifapentine"	"Antimycobacterials"	"J04AB05,QJ04AB05"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifp,rpt"	"prifitin,priftin,rifapentin,rifapentina,rifapentinum"	0.11	"g"			"100059-5,76627-9"
-"RFX"	6436173	"Rifaximin"	"Other antibacterials"	"A07AA11,D06AX11,QA07AA11,QD06AX11,QG51AA06,QJ51XX01"	"Intestinal antiinfectives"	"Antibiotics"	"NA"	"fatroximin,flonorm,lormyx,lumenax,normix,rifacol,rifamixin,rifaxidin,rifaximina,rifaximine,rifaximinum,rifaxin,ritacol,spiraxin,xifaxan,xifaxsan"	0.6	"g"			"73589-4,73611-6,73634-8"
-"RIT"	65633	"Ritipenem"	"Carbapenems"	"NA"			"NA"	"ritipenemsalt"					"NA"
-"RIA"	163692	"Ritipenem acoxil"	"Carbapenems"	"NA"			"NA"	"penemac"					"NA"
-"ROK"	5282211	"Rokitamycin"	"Macrolides/lincosamides"	"J01FA12,QJ01FA12"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"rokita"	"propionylleucomycin,ricamycin,rokicid,rokital,rokitamicina,rokitamycine,rokitamycinum"	0.8	"g"			"NA"
+"RID1"	16659285	"Ridinilazole"	"Other"	"NA"			"NA"	"ridinilazol"					"NA"
+"RIB"	135398743	"Rifabutin"	"Rifamycins,Antimycobacterials"	"J04AB04,QJ04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"ansamy,rfb,rifb"	"alfacid,ansamicin,ansamycins,ansatipin,ansatipine,assatipin,mycobutin,rifabutinum"	0.15	"g"			"100699-8,16100-0,16386-5,16387-3,19149-4,20386-9,23630-7,24032-5,25199-1,25200-7,25201-5,42655-1,42656-9,54183-9,96113-6"
+"RIF"	135398735	"Rifampicin"	"Rifamycins,Antimycobacterials"	"J04AB02,QJ04AB02,QJ54AB02"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifa,rifamp"	"abrifam,archidyn,arficin,arzide,benemicin,doloresum,eremfat,famcin,fenampicin,rifadin,rifadine,rifagen,rifaldazin,rifaldazine,rifaldin,rifam,rifamor,rifampicina,rifampicine,rifampicinum,rifampin,rifamsolin,rifapiam,rifaprodin,rifcin,rifinah,rifobac,rifoldin,rifoldine,riforal,rimactan,rimactane,rimactazid,rimactizid,rimazid,sinerdol,tubocin"	0.6	"g"	0.6	"g"	"NA"
+"REI"	135483893	"Rifampicin/ethambutol/isoniazid"	"Rifamycins,Antimycobacterials"	"J04AM07,QJ04AM07"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"isonarif,rifamate,rifamazid"					"NA"
+"RFI"		"Rifampicin/isoniazid"	"Rifamycins,Antimycobacterials"	"J04AM02,QJ04AM02"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
+"RPEI"		"Rifampicin/pyrazinamide/ethambutol/isoniazid"	"Rifamycins,Antimycobacterials"	"J04AM06,QJ04AM06"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
+"RPI"		"Rifampicin/pyrazinamide/isoniazid"	"Rifamycins,Antimycobacterials"	"J04AM05,QJ04AM05"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
+"RFM"	6324616	"Rifamycin"	"Rifamycins,Antimycobacterials"	"A07AA13,D06AX15,J04AB03,QA07AA13,QD06AX15,QJ04AB03,QJ54AB03,QS01AA16,QS02AA12,S01AA16,S02AA12"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifmyc"	"aemcolo,nacimycin,nancimycin,otofa,rifamastene,rifamicina,rifamycine,rifamycinum,rifocin,rifocyn,tuborin"	0.8	"g"	0.6	"g"	"NA"
+"RFP"	135403821	"Rifapentine"	"Rifamycins,Antimycobacterials"	"J04AB05,QJ04AB05"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifp,rpt"	"prifitin,priftin,rifapentin,rifapentina,rifapentinum"	0.11	"g"			"100059-5,76627-9"
+"RFX"	6436173	"Rifaximin"	"Other"	"A07AA11,D06AX11,QA07AA11,QD06AX11,QG51AA06,QJ51XX01"	"Intestinal antiinfectives"	"Antibiotics"	"NA"	"fatroximin,flonorm,lormyx,lumenax,normix,rifacol,rifamixin,rifaxidin,rifaximina,rifaximine,rifaximinum,rifaxin,ritacol,spiraxin,xifaxan,xifaxsan"	0.6	"g"			"73589-4,73611-6,73634-8"
+"RIT"	65633	"Ritipenem"	"Carbapenems,Beta-lactams"	"NA"			"NA"	"ritipenemsalt"					"NA"
+"RIA"	163692	"Ritipenem acoxil"	"Carbapenems,Beta-lactams"	"NA"			"NA"	"penemac"					"NA"
+"ROK"	5282211	"Rokitamycin"	"Macrolides"	"J01FA12,QJ01FA12"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"rokita"	"propionylleucomycin,ricamycin,rokicid,rokital,rokitamicina,rokitamycine,rokitamycinum"	0.8	"g"			"NA"
 "RLT"	54682938	"Rolitetracycline"	"Tetracyclines"	"J01AA09,QJ01AA09"	"Tetracyclines"	"Tetracyclines"	"NA"	"bristacin,colbiocin,kinteto,reverin,revrin,rolitetraciclina,rolitetracyclinum,solvocillin,superciclin,synotodecin,synterin,syntetrex,syntetrin,tetraverin,transcycline,velacicline,velacycline"			0.35	"g"	"18976-1,435-8,436-6,437-4,438-2"
 "ROS"	287180	"Rosoxacin"	"Quinolones"	"J01MB01,QJ01MB01"	"Quinolone antibacterials"	"Other quinolones"	"NA"	"acrosoxacin,eracine,eradacil,eradacin,eradicin,rosoxacine,rosoxacino,rosoxacinum,roxadyl,winoxacin,winuron"	0.3	"g"			"18977-9,439-0,440-8,441-6,442-4,55713-2"
-"RXT"		"Roxithromycin"	"Macrolides/lincosamides"	"J01FA06,QJ01FA06"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"roxi,roxith"	"NA"	0.3	"g"			"18978-7,443-2,444-0,445-7,446-5,7046-6"
-"RFL"	58258	"Rufloxacin"	"Fluoroquinolones"	"J01MA10,QJ01MA10"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"monos,rufloxacine,rufloxacino,rufloxacinum,tebraxin,uroflox"	0.2	"g"			"NA"
-"SAL"	3085092	"Salinomycin"	"Other antibacterials"	"QP51BB01"			"salino"	"coxistac,procoxacin,salinomicina,salinomycine,salinomycinum"					"35836-6,35837-4,35838-2,87593-0"
-"SAR"	56208	"Sarafloxacin"	"Fluoroquinolones"	"QJ01MA98"			"sarafl"	"difloxacino,difloxacinum,difloxcine,sarafin,saraflox,sarafloxacine,sarafloxacino,sarafloxacinum"					"73588-6,73610-8,73633-0"
+"RXT"		"Roxithromycin"	"Macrolides"	"J01FA06,QJ01FA06"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"roxi,roxith"	"NA"	0.3	"g"			"18978-7,443-2,444-0,445-7,446-5,7046-6"
+"RFL"	58258	"Rufloxacin"	"Fluoroquinolones,Quinolones"	"J01MA10,QJ01MA10"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"monos,rufloxacine,rufloxacino,rufloxacinum,tebraxin,uroflox"	0.2	"g"			"NA"
+"SAL"	3085092	"Salinomycin"	"Other"	"QP51BB01"			"salino"	"coxistac,procoxacin,salinomicina,salinomycine,salinomycinum"					"35836-6,35837-4,35838-2,87593-0"
+"SAR"	56208	"Sarafloxacin"	"Fluoroquinolones,Quinolones"	"QJ01MA98"			"sarafl"	"difloxacino,difloxacinum,difloxcine,sarafin,saraflox,sarafloxacine,sarafloxacino,sarafloxacinum"					"73588-6,73610-8,73633-0"
 "SRC"	54681908	"Sarecycline"	"Tetracyclines"	"J01AA14,QJ01AA14"	"Tetracyclines"	"Tetracyclines"	"NA"	"sareciclina,seysara"	0.1	"g"			"NA"
-"SRX"	9933415	"Sarmoxicillin"	"Beta-lactams/penicillins"	"NA"			"NA"	"sarmoxillina,sarmoxilline,sarmoxillinum"					"NA"
-"SEC"	71815	"Secnidazole"	"Other antibacterials"	"P01AB07"			"NA"	"flagentyl,secnidal,secnidazolum,secnil,sindose,solosec"	2	"g"			"NA"
-"SMF"		"Simvastatin/fenofibrate"	"Antimycobacterials"	"C10BA04,QC10BA04"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"simv"	"NA"					"NA"
+"SRX"	9933415	"Sarmoxicillin"	"Penicillins,Beta-lactams"	"NA"			"NA"	"sarmoxillina,sarmoxilline,sarmoxillinum"					"NA"
+"SEC"	71815	"Secnidazole"	"Other"	"P01AB07"			"NA"	"flagentyl,secnidal,secnidazolum,secnil,sindose,solosec"	2	"g"			"NA"
 "SIS"	36119	"Sisomicin"	"Aminoglycosides"	"J01GB08,QJ01GB08"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"siso,sisomy"	"rickamicin,salvamina,sisomicina,sisomicine,sisomicinum,sisomin,sisomycin,sissomicin,sizomycin"			0.24	"g"	"18979-5,447-3,448-1,449-9,450-7,55714-0"
-"SIT"	461399	"Sitafloxacin"	"Fluoroquinolones"	"J01MA21,QJ01MA21"			"sitafl"	"gracevit"	0.1	"g"			"NA"
+"SIT"	461399	"Sitafloxacin"	"Fluoroquinolones,Quinolones"	"J01MA21,QJ01MA21"			"sitafl"	"gracevit"	0.1	"g"			"NA"
 "SDA"	2724368	"Sodium aminosalicylate"	"Antimycobacterials"	"J04AA02,QJ04AA02"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	"NA"	"bactylan,lepasen,monopas,tubersan"	14	"g"	14	"g"	"NA"
-"SOL"	25242512	"Solithromycin"	"Macrolides/lincosamides"	"J01FA16,QJ01FA16"			"NA"	"solithera"					"73587-8,73609-0,73632-2"
-"SPX"	60464	"Sparfloxacin"	"Fluoroquinolones"	"J01MA09,QJ01MA09"	"Quinolone antibacterials"	"Fluoroquinolones"	"spa,spar,sparfl"	"esparfloxacino,parox,spara,sparfloxacine,sparfloxacinum,zagam"	0.2	"g"			"20397-6,23610-9,23628-1,35839-0,7047-4"
-"SPT"	15541	"Spectinomycin"	"Other antibacterials"	"J01XX04,QJ01XX04"	"Other antibacterials"	"Other antibacterials"	"sc,spe,spec,spect,spt"	"actinospectacina,adspec,espectinomicina,prospec,spectam,spectinomicina,spectinomycine,spectinomycinhydrate,spectinomycinum,spectogard,stanilo,togamycin,trobicin"			3	"g"	"18980-3,35840-8,451-5,452-3,453-1,454-9"
-"SPI"	6419898	"Spiramycin"	"Macrolides/lincosamides"	"J01FA02,QJ01FA02,QJ51FA02"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"sipram,spir,spiram"	"formacidine"	3	"g"			"18981-1,455-6,456-4,457-2,458-0,55715-7"
-"SPM"		"Spiramycin/metronidazole"	"Other antibacterials"	"J01RA04,QJ01RA04"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"SOL"	25242512	"Solithromycin"	"Macrolides"	"J01FA16,QJ01FA16"			"NA"	"solithera"					"73587-8,73609-0,73632-2"
+"SPX"	60464	"Sparfloxacin"	"Fluoroquinolones,Quinolones"	"J01MA09,QJ01MA09"	"Quinolone antibacterials"	"Fluoroquinolones"	"spa,spar,sparfl"	"esparfloxacino,parox,spara,sparfloxacine,sparfloxacinum,zagam"	0.2	"g"			"20397-6,23610-9,23628-1,35839-0,7047-4"
+"SPT"	15541	"Spectinomycin"	"Other"	"J01XX04,QJ01XX04"	"Other antibacterials"	"Other antibacterials"	"sc,spe,spec,spect,spt"	"actinospectacina,adspec,espectinomicina,prospec,spectam,spectinomicina,spectinomycine,spectinomycinhydrate,spectinomycinum,spectogard,stanilo,togamycin,trobicin"			3	"g"	"18980-3,35840-8,451-5,452-3,453-1,454-9"
+"SPI"	6419898	"Spiramycin"	"Macrolides"	"J01FA02,QJ01FA02,QJ51FA02"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"sipram,spir,spiram"	"formacidine"	3	"g"			"18981-1,455-6,456-4,457-2,458-0,55715-7"
+"SPM"		"Spiramycin/metronidazole"	"Other"	"J01RA04,QJ01RA04"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
 "STR"		"Streptoduocin"	"Aminoglycosides"	"J01GA02,QJ01GA02"	"Aminoglycoside antibacterials"	"Streptomycins"	"NA"	"NA"			1	"g"	"NA"
 "STR1"	19649	"Streptomycin"	"Aminoglycosides"	"A07AA04,J01GA01,QA07AA04,QJ01GA01"	"Aminoglycoside antibacterials"	"Streptomycins"	"s,st1000,st2000,stm,str,stre,strept"	"agrept,agrimycin,chemform,estreptomicina,gerox,neodiestreptopab,strepcen,streptomicina,streptomycine,streptomycinum,streptomyzin"			1	"g"	"18982-9,18983-7,20462-8,23626-5,25185-0,25205-6,25206-4,35841-6,4039-4,42658-5,42659-3,459-8,460-6,461-4,462-2,46719-1,48177-0,6933-6,7048-2,7049-0,96114-4"
 "STH"		"Streptomycin-high"	"Aminoglycosides"	"NA"			"sthi,sthl,strepto high,streptomycin high"	"NA"					"18983-7,35841-6,6933-6,7049-0"
 "STI"		"Streptomycin/isoniazid"	"Antimycobacterials"	"J04AM01,QJ04AM01"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
-"SUL"	130313	"Sulbactam"	"Beta-lactams/penicillins"	"J01CG01,QJ01CG01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"sulbac"	"betamaze,sulbactamum"			1	"g"	"41716-2,41717-0,41718-8,41739-4"
-"SBC"	20055036	"Sulbenicillin"	"Beta-lactams/penicillins"	"J01CA16,QJ01CA16"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"sulben"	"kedacillin,kedacillina,sulbenicilina,sulbenicilline,sulbenicillinum,sulpelin"			15	"g"	"NA"
-"SUC"	5318	"Sulconazole"	"Antifungals/antimycotics"	"D01AC09,QD01AC09"			"NA"	"sulconazol,sulconazolum"					"NA"
-"SUP"	6634	"Sulfachlorpyridazine"	"Other antibacterials"	"QJ01EQ12"			"sulchl"	"cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone,solfaclorpiridazina,sonilyn,sulfacloropiridazina,sulfaclorpiridazina,vetisulid"					"NA"
-"SDI"	5215	"Sulfadiazine"	"Trimethoprims"	"J01EC02,QJ01EQ10"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"suldia"	"codiazine,cremodiazine,cremotres,debenal,deltazina,dermazin,dermazine,diazolone,diazovit,eskadiazine,flamazine,geben,liquadiazine,microsulfon,neazine,neotrizine,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,silbertone,sildaflo,silvadene,silvazine,silver,silveramide,sliverex,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonsol,sulfose,sulphadiazine,terfonyl,theradiazine,thermazene,trifonamide,trisem,truozine"	0.6	"g"			"18984-5,27216-1,463-0,464-8,465-5,466-3,59742-7,6907-0,7050-8"
-"SLT"	122284	"Sulfadiazine/tetroxoprim"	"Trimethoprims"	"J01EE06"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"berlocombin,cotetroxazine,potesept,trimerazine"					"NA"
-"SLT1"	64932	"Sulfadiazine/trimethoprim"	"Trimethoprims"	"J01EE02,QJ01EW10,QJ51RE01"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"antastmon,astra,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim"					"NA"
-"SUD"	5323	"Sulfadimethoxine"	"Trimethoprims"	"J01ED01,QJ01EQ09,QP51BA01"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"sdimet"	"abcid,agribon,albon,arnosulfan,bactotril,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,fuxal,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamidesalt,omnibon,persulfen,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxinesalt,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfoplan,sulforal,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon"	0.5	"g"			"87799-3,87803-3"
-"SDM"	5327	"Sulfadimidine"	"Trimethoprims"	"J01EB03,QJ01EQ03,QP51AG01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"suldim"	"azolmetazin,bovibol,calfspan,cremomethazine,diazil,diazilsulfadine,diazyl,dimezathine,intradine,kelametazine,mermeth,neasina,neazina,panazin,pirmazin,primazin,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidinum,sulfadimidinun,sulfadine,sulfametazina,sulfametazyny,sulfamethiazine,sulfamezathine,sulfamidine,sulfodimesin,sulfodimezine,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan,vesadin"	4	"g"			"NA"
-"SLT2"		"Sulfadimidine/trimethoprim"	"Trimethoprims"	"J01EE05,QJ01EW03"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"NA"					"NA"
-"SLF"	5344	"Sulfafurazole"	"Trimethoprims"	"J01EB05,QJ01EQ05,QS01AB02,S01AB02"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sfsz"	"accuzole,alphazole,amidoxal,astrazolo,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,entusil,entusul,ganda,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazol,novazolo,novosaxazole,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxoxol,saxosozine,sodizole,solfafurazolo,sosol,soxamide,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafurazol,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan"	4	"g"	4	"g"	"NA"
-"SLF1"	5343	"Sulfaisodimidine"	"Trimethoprims"	"J01EB01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"aristamid,aristamide,aristogyn,domain,domian,elcosin,elcosine,elkosil,elkosin,elkosine,erycon,isosulf,mefenal,solfisomidina,sulfadimetine,sulfaisodimerazine,sulfaisodimidinum,sulfaisomidine,sulfasomidine,sulfisomidin,sulfisomidina,sulfisomidine,sulfisomidinum,sulphasomidine"	4	"g"	4	"g"	"NA"
-"SLF2"	9047	"Sulfalene"	"Trimethoprims"	"J01ED02,QJ01EQ19"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"dalysep,farmitalia,kelfizin,kelfizina,kelfizine,policydal,solfametopirazina,sulfalen,sulfaleno,sulfalenum,sulfamethopyrazine,sulfamethoxypyrazine,sulfametopyrazine,sulfametoxypyridazin,sulphalene,sulphametopyrazine,vetkelfizina"	0.1	"g"			"NA"
-"SZO"	187764	"Sulfamazone"	"Trimethoprims"	"J01ED09"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"sulfamazona,sulfamazonum,sulfenazone"	1.5	"g"			"NA"
-"SLF3"	5325	"Sulfamerazine"	"Trimethoprims"	"D06BA06,J01ED07,QD06BA06,QJ01EQ17"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"sulmet"	"cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine"	3	"g"			"NA"
-"SLT3"		"Sulfamerazine/trimethoprim"	"Trimethoprims"	"J01EE07,QJ01EW18"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"NA"					"NA"
-"SUM"	5327	"Sulfamethazine"	"Other antibacterials"	"NA"			"NA"	"NA"					"87592-2"
-"SLF4"	5328	"Sulfamethizole"	"Trimethoprims"	"B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sfmz"	"aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin"	4	"g"			"60175-7,60176-5,60177-3"
-"SMX"	5329	"Sulfamethoxazole"	"Trimethoprims"	"J01EC01,QJ01EQ11"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"sfmx,sulf,sulfam"	"septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,sulphisomezole,urobak"	2	"g"			"10342-4,11577-4,18985-2,25271-8,39772-9,467-1,468-9,469-7,470-5,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
-"SLF5"	5330	"Sulfamethoxypyridazine"	"Trimethoprims"	"J01ED05,QJ01EQ15"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces"	0.5	"g"			"NA"
-"SLF6"	19596	"Sulfametomidine"	"Trimethoprims"	"J01ED03"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"duroprocin,methofadin,methofazine,solfametomidina,sulfametomidin,sulfametomidina,sulfametomidinum,telemid"					"NA"
-"SLF7"	5326	"Sulfametoxydiazine"	"Trimethoprims"	"J01ED04"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,kiron,longasulf,methoxypyrimal,solfametossidiazina,sulfameter,sulfametersalt,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazinum,sulla,sulphameter,sulphamethoxydiazine,supramid,ultrax"	0.5	"g"			"NA"
-"SLT4"		"Sulfametrole/trimethoprim"	"Trimethoprims"	"J01EE03"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"trsm"	"NA"					"NA"
-"SLF8"	12894	"Sulfamoxole"	"Trimethoprims"	"J01EC03"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"NA"	"enterocura,justamil,oxasulfa,solfaguanolo,solfamossolo,sulfadimethyloxazole,sulfaguanol,sulfaguanole,sulfaguanolum,sulfamoxol,sulfamoxolum,sulfano,sulfavigor,sulfmidil,sulfono,sulfune,sulfuno,sulphamoxole,tardamid,tardamide"	1	"g"	1	"g"	"NA"
-"SLT5"		"Sulfamoxole/trimethoprim"	"Trimethoprims"	"J01EE04"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"NA"					"NA"
-"SLF9"	5333	"Sulfanilamide"	"Trimethoprims"	"D06BA05,J01EB06,QD06BA05,QJ01EQ06"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"albexan,albosal,ambeside,antistrept,astreptine,astrocid,bacteramid,bactesid,collomide,colsulanyde,copticide,deseptyl,dipron,ergaseptine,erysipan,estreptocida,exoseptoplix,fourneau,gerison,gombardol,hydroxysulfonamide,infepan,lusil,lysococcine,neococcyl,orgaseptine,prontalbin,prontylin,proseptal,proseptine,proseptol,pysococcine,sanamid,septanilam,septinal,septolix,septoplex,septoplix,solfanilamide,stramid,strepamide,strepsan,streptagol,streptamid,streptamin,streptasol,streptocid,streptocide,streptocidum,streptoclase,streptocom,strepton,streptopan,streptosil,streptozol,streptozone,streptrocide,sulfamidyl,sulfamine,sulfana,sulfanalone,sulfanidyl,sulfanil,sulfanilamida,sulfanilamidomethan,sulfanilamidum,sulfanimide,sulfocidin,sulfocidine,sulfonylamide,sulphanilamide,sulphanilamidum,sulphonamide,therapol,tolder"					"NA"
-"SLF10"	68933	"Sulfaperin"	"Trimethoprims"	"J01ED06"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"anastaf,archisulfa,archisulpha,avissul,chemiopen,demosulfan,demosulphan,durisan,isosulfamerazine,isosulphamerazine,methylsulfadiazin,methylsulfadiazine,methylsulphadiazine,novosul,orosulfan,pallidin,retardon,risulfasens,sulfaperina,sulfaperine,sulfaperinum,sulfatreis,sulfopirimidine,sulpenta,sulphaperin,sulphaperina,sulphaperinum"	0.5	"g"			"NA"
-"SLF11"	5335	"Sulfaphenazole"	"Trimethoprims"	"J01ED08,QJ01EQ08"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"depocid,depotsulfonamide,eftolon,firmazolo,inamil,isarol,merian,orisul,orisulf,paidazolo,phenylsulfapyrazole,plisulfan,raziosulfa,solfafenazolo,sulfabid,sulfafenazol,sulfafenazolo,sulfaphenazol,sulfaphenazolum,sulfaphenazon,sulfaphenylpipazol,sulfaphenylpyrazol,sulfaphenylpyrazole,sulfonylpyrazol,sulphaphenazole,sulphenazole"	1	"g"			"NA"
-"SLF12"	5336	"Sulfapyridine"	"Trimethoprims"	"J01EB04,QJ01EQ04"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"adiplon,coccoclase,dagenan,eubasin,eubasinum,haptocil,piridazol,plurazol,pyriamid,pyridazol,relbapiridina,ronin,septipulmon,solfapiridina,soludagenan,streptosilpyridine,sulfapiridina,sulfapyridin,sulfapyridinum,sulfidin,sulfidine,sulphapyridin,sulphapyridine,thioseptal,trianon"	1	"g"			"14075-6,55580-5"
-"SNA"	60582	"Sulfasuccinamide"	"Other antibacterials"	"NA"			"NA"	"sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum"					"NA"
-"SUT"	5340	"Sulfathiazole"	"Trimethoprims"	"D06BA02,J01EB07,QD06BA02,QJ01EQ07"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sulthi"	"azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole"					"87591-4,87796-9,87797-7"
-"SLF13"	3000579	"Sulfathiourea"	"Trimethoprims"	"J01EB08"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea"	6	"g"			"NA"
-"SOX"	5344	"Sulfisoxazole"	"Other antibacterials"	"NA"			"sulfiz"	"NA"					"11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
-"SSS"	86225	"Sulfonamide"	"Other antibacterials"	"NA"			"sfna,sulami"	"NA"					"17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2"
-"SLP"	9950244	"Sulopenem"	"Other antibacterials"	"NA"			"sulope"	"orlynvah"					"55289-3,55290-1,55291-9"
-"SLT6"	444022	"Sultamicillin"	"Beta-lactams/penicillins"	"J01CR04,QJ01CR04"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"sultos"	"combisid,sultamicilina,sultamicilline,sultamicillinum,unacid"	1.5	"g"			"NA"
-"SUR"	46700778	"Surotomycin"	"Other antibacterials"	"NA"			"NA"	"surotomicina,surotomycine"					"NA"
-"TAL"	71447	"Talampicillin"	"Beta-lactams/penicillins"	"J01CA15,QJ01CA15"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"aseocillin,phthalidyl,talampicilina,talampicilline,talampicillinum,talpen,yamacillin"	2	"g"			"18988-6,479-6,480-4,481-2,482-0"
-"TLP"	163307	"Talmetoprim"	"Other antibacterials"	"NA"			"NA"	"NA"					"NA"
-"TAZ"	123630	"Tazobactam"	"Beta-lactams/penicillins"	"J01CG02,QJ01CG02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"tazo,tazoba"	"exblifep,tazobactamsalt,tazobactamum,tazobactum"					"41719-6,41720-4,41721-2,41740-2"
-"TBP"	9800194	"Tebipenem"	"Carbapenems"	"NA"			"NA"	"NA"					"NA"
+"SUL"	130313	"Sulbactam"	"Beta-lactamase inhibitors"	"J01CG01,QJ01CG01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"sulbac"	"betamaze,sulbactamum"			1	"g"	"41716-2,41717-0,41718-8,41739-4"
+"SBC"	20055036	"Sulbenicillin"	"Penicillins,Beta-lactams"	"J01CA16,QJ01CA16"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"sulben"	"kedacillin,kedacillina,sulbenicilina,sulbenicilline,sulbenicillinum,sulpelin"			15	"g"	"NA"
+"SUC"	5318	"Sulconazole"	"Antifungals"	"D01AC09,QD01AC09"			"NA"	"sulconazol,sulconazolum"					"NA"
+"SUP"	6634	"Sulfachlorpyridazine"	"Sulfonamides"	"QJ01EQ12"			"sulchl"	"cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone,solfaclorpiridazina,sonilyn,sulfacloropiridazina,sulfaclorpiridazina,vetisulid"					"NA"
+"SDI"	5215	"Sulfadiazine"	"Trimethoprims,Sulfonamides"	"J01EC02,QJ01EQ10"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"suldia"	"codiazine,cremodiazine,cremotres,debenal,deltazina,dermazin,dermazine,diazolone,diazovit,eskadiazine,flamazine,geben,liquadiazine,microsulfon,neazine,neotrizine,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,silbertone,sildaflo,silvadene,silvazine,silver,silveramide,sliverex,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonsol,sulfose,sulphadiazine,terfonyl,theradiazine,thermazene,trifonamide,trisem,truozine"	0.6	"g"			"18984-5,27216-1,463-0,464-8,465-5,466-3,59742-7,6907-0,7050-8"
+"SLT"	122284	"Sulfadiazine/tetroxoprim"	"Trimethoprims,Sulfonamides"	"J01EE06"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"berlocombin,cotetroxazine,potesept,trimerazine"					"NA"
+"SLT1"	64932	"Sulfadiazine/trimethoprim"	"Trimethoprims,Sulfonamides"	"J01EE02,QJ01EW10,QJ51RE01"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"antastmon,astra,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim"					"NA"
+"SUD"	5323	"Sulfadimethoxine"	"Trimethoprims,Sulfonamides"	"J01ED01,QJ01EQ09,QP51BA01"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"sdimet"	"abcid,agribon,albon,arnosulfan,bactotril,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,fuxal,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamidesalt,omnibon,persulfen,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxinesalt,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfoplan,sulforal,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon"	0.5	"g"			"87799-3,87803-3"
+"SDM"	5327	"Sulfadimidine"	"Trimethoprims,Sulfonamides"	"J01EB03,QJ01EQ03,QP51AG01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"suldim"	"azolmetazin,bovibol,calfspan,cremomethazine,diazil,diazilsulfadine,diazyl,dimezathine,intradine,kelametazine,mermeth,neasina,neazina,panazin,pirmazin,primazin,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidinum,sulfadimidinun,sulfadine,sulfametazina,sulfametazyny,sulfamethiazine,sulfamezathine,sulfamidine,sulfodimesin,sulfodimezine,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan,vesadin"	4	"g"			"NA"
+"SLT2"		"Sulfadimidine/trimethoprim"	"Trimethoprims,Sulfonamides"	"J01EE05,QJ01EW03"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"NA"					"NA"
+"SLF"	5344	"Sulfafurazole"	"Trimethoprims,Sulfonamides"	"J01EB05,QJ01EQ05,QS01AB02,S01AB02"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sfsz"	"accuzole,alphazole,amidoxal,astrazolo,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,entusil,entusul,ganda,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazol,novazolo,novosaxazole,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxoxol,saxosozine,sodizole,solfafurazolo,sosol,soxamide,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafurazol,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan"	4	"g"	4	"g"	"NA"
+"SLF1"	5343	"Sulfaisodimidine"	"Trimethoprims,Sulfonamides"	"J01EB01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"aristamid,aristamide,aristogyn,domain,domian,elcosin,elcosine,elkosil,elkosin,elkosine,erycon,isosulf,mefenal,solfisomidina,sulfadimetine,sulfaisodimerazine,sulfaisodimidinum,sulfaisomidine,sulfasomidine,sulfisomidin,sulfisomidina,sulfisomidine,sulfisomidinum,sulphasomidine"	4	"g"	4	"g"	"NA"
+"SLF2"	9047	"Sulfalene"	"Trimethoprims,Sulfonamides"	"J01ED02,QJ01EQ19"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"dalysep,farmitalia,kelfizin,kelfizina,kelfizine,policydal,solfametopirazina,sulfalen,sulfaleno,sulfalenum,sulfamethopyrazine,sulfamethoxypyrazine,sulfametopyrazine,sulfametoxypyridazin,sulphalene,sulphametopyrazine,vetkelfizina"	0.1	"g"			"NA"
+"SZO"	187764	"Sulfamazone"	"Trimethoprims,Sulfonamides"	"J01ED09"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"sulfamazona,sulfamazonum,sulfenazone"	1.5	"g"			"NA"
+"SLF3"	5325	"Sulfamerazine"	"Trimethoprims,Sulfonamides"	"D06BA06,J01ED07,QD06BA06,QJ01EQ17"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"sulmet"	"cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine"	3	"g"			"NA"
+"SLT3"		"Sulfamerazine/trimethoprim"	"Trimethoprims,Sulfonamides"	"J01EE07,QJ01EW18"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"NA"					"NA"
+"SUM"	5327	"Sulfamethazine"	"Sulfonamides"	"NA"			"NA"	"NA"					"87592-2"
+"SLF4"	5328	"Sulfamethizole"	"Trimethoprims,Sulfonamides"	"B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sfmz"	"aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin"	4	"g"			"60175-7,60176-5,60177-3"
+"SMX"	5329	"Sulfamethoxazole"	"Trimethoprims,Sulfonamides"	"J01EC01,QJ01EQ11"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"sfmx,sulf,sulfam"	"septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,sulphisomezole,urobak"	2	"g"			"10342-4,11577-4,18985-2,25271-8,39772-9,467-1,468-9,469-7,470-5,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
+"SLF5"	5330	"Sulfamethoxypyridazine"	"Trimethoprims,Sulfonamides"	"J01ED05,QJ01EQ15"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces"	0.5	"g"			"NA"
+"SLF6"	19596	"Sulfametomidine"	"Trimethoprims,Sulfonamides"	"J01ED03"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"duroprocin,methofadin,methofazine,solfametomidina,sulfametomidin,sulfametomidina,sulfametomidinum,telemid"					"NA"
+"SLF7"	5326	"Sulfametoxydiazine"	"Trimethoprims,Sulfonamides"	"J01ED04"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,kiron,longasulf,methoxypyrimal,solfametossidiazina,sulfameter,sulfametersalt,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazinum,sulla,sulphameter,sulphamethoxydiazine,supramid,ultrax"	0.5	"g"			"NA"
+"SLT4"		"Sulfametrole/trimethoprim"	"Trimethoprims,Sulfonamides"	"J01EE03"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"trsm"	"NA"					"NA"
+"SLF8"	12894	"Sulfamoxole"	"Trimethoprims,Sulfonamides"	"J01EC03"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"NA"	"enterocura,justamil,oxasulfa,solfaguanolo,solfamossolo,sulfadimethyloxazole,sulfaguanol,sulfaguanole,sulfaguanolum,sulfamoxol,sulfamoxolum,sulfano,sulfavigor,sulfmidil,sulfono,sulfune,sulfuno,sulphamoxole,tardamid,tardamide"	1	"g"	1	"g"	"NA"
+"SLT5"		"Sulfamoxole/trimethoprim"	"Trimethoprims,Sulfonamides"	"J01EE04"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"NA"					"NA"
+"SLF9"	5333	"Sulfanilamide"	"Trimethoprims,Sulfonamides"	"D06BA05,J01EB06,QD06BA05,QJ01EQ06"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"albexan,albosal,ambeside,antistrept,astreptine,astrocid,bacteramid,bactesid,collomide,colsulanyde,copticide,deseptyl,dipron,ergaseptine,erysipan,estreptocida,exoseptoplix,fourneau,gerison,gombardol,hydroxysulfonamide,infepan,lusil,lysococcine,neococcyl,orgaseptine,prontalbin,prontylin,proseptal,proseptine,proseptol,pysococcine,sanamid,septanilam,septinal,septolix,septoplex,septoplix,solfanilamide,stramid,strepamide,strepsan,streptagol,streptamid,streptamin,streptasol,streptocid,streptocide,streptocidum,streptoclase,streptocom,strepton,streptopan,streptosil,streptozol,streptozone,streptrocide,sulfamidyl,sulfamine,sulfana,sulfanalone,sulfanidyl,sulfanil,sulfanilamida,sulfanilamidomethan,sulfanilamidum,sulfanimide,sulfocidin,sulfocidine,sulfonylamide,sulphanilamide,sulphanilamidum,sulphonamide,therapol,tolder"					"NA"
+"SLF10"	68933	"Sulfaperin"	"Trimethoprims,Sulfonamides"	"J01ED06"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"anastaf,archisulfa,archisulpha,avissul,chemiopen,demosulfan,demosulphan,durisan,isosulfamerazine,isosulphamerazine,methylsulfadiazin,methylsulfadiazine,methylsulphadiazine,novosul,orosulfan,pallidin,retardon,risulfasens,sulfaperina,sulfaperine,sulfaperinum,sulfatreis,sulfopirimidine,sulpenta,sulphaperin,sulphaperina,sulphaperinum"	0.5	"g"			"NA"
+"SLF11"	5335	"Sulfaphenazole"	"Trimethoprims,Sulfonamides"	"J01ED08,QJ01EQ08"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"depocid,depotsulfonamide,eftolon,firmazolo,inamil,isarol,merian,orisul,orisulf,paidazolo,phenylsulfapyrazole,plisulfan,raziosulfa,solfafenazolo,sulfabid,sulfafenazol,sulfafenazolo,sulfaphenazol,sulfaphenazolum,sulfaphenazon,sulfaphenylpipazol,sulfaphenylpyrazol,sulfaphenylpyrazole,sulfonylpyrazol,sulphaphenazole,sulphenazole"	1	"g"			"NA"
+"SLF12"	5336	"Sulfapyridine"	"Trimethoprims,Sulfonamides"	"J01EB04,QJ01EQ04"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"adiplon,coccoclase,dagenan,eubasin,eubasinum,haptocil,piridazol,plurazol,pyriamid,pyridazol,relbapiridina,ronin,septipulmon,solfapiridina,soludagenan,streptosilpyridine,sulfapiridina,sulfapyridin,sulfapyridinum,sulfidin,sulfidine,sulphapyridin,sulphapyridine,thioseptal,trianon"	1	"g"			"14075-6,55580-5"
+"SNA"	60582	"Sulfasuccinamide"	"Sulfonamides"	"NA"			"NA"	"sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum"					"NA"
+"SUT"	5340	"Sulfathiazole"	"Trimethoprims,Sulfonamides"	"D06BA02,J01EB07,QD06BA02,QJ01EQ07"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sulthi"	"azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole"					"87591-4,87796-9,87797-7"
+"SLF13"	3000579	"Sulfathiourea"	"Trimethoprims,Sulfonamides"	"J01EB08"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea"	6	"g"			"NA"
+"SOX"	5344	"Sulfisoxazole"	"Sulfonamides"	"NA"			"sulfiz"	"NA"					"11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
+"SSS"	86225	"Sulfonamide"	"Sulfonamides"	"NA"			"sfna,sulami"	"NA"					"17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2"
+"SLP"	9950244	"Sulopenem"	"Other"	"NA"			"sulope"	"orlynvah"					"55289-3,55290-1,55291-9"
+"SLT6"	444022	"Sultamicillin"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"J01CR04,QJ01CR04"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"sultos"	"combisid,sultamicilina,sultamicilline,sultamicillinum,unacid"	1.5	"g"			"NA"
+"SUR"	46700778	"Surotomycin"	"Other"	"NA"			"NA"	"surotomicina,surotomycine"					"NA"
+"TAL"	71447	"Talampicillin"	"Penicillins,Beta-lactams"	"J01CA15,QJ01CA15"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"NA"	"aseocillin,phthalidyl,talampicilina,talampicilline,talampicillinum,talpen,yamacillin"	2	"g"			"18988-6,479-6,480-4,481-2,482-0"
+"TLP"	163307	"Talmetoprim"	"Other"	"NA"			"NA"	"NA"					"NA"
+"TAN"	76902493	"Taniborbactam"	"Carbapenems,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"vnrx-5133"	"NA"					"NA"
+"TAZ"	123630	"Tazobactam"	"Beta-lactamase inhibitors"	"J01CG02,QJ01CG02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"tazo,tazoba"	"exblifep,tazobactamsalt,tazobactamum,tazobactum"					"41719-6,41720-4,41721-2,41740-2"
+"TBP"	9800194	"Tebipenem"	"Carbapenems,Beta-lactams"	"NA"			"NA"	"NA"					"NA"
 "TZD"	11234049	"Tedizolid"	"Oxazolidinones"	"J01XX11,QJ01XX11"	"Other antibacterials"	"Other antibacterials"	"tedi"	"torezolid"	0.2	"g"	0.2	"g"	"73586-0,73608-2,73631-4"
 "TEC"	16131923	"Teicoplanin"	"Glycopeptides"	"J01XA02,QJ01XA02"	"Other antibacterials"	"Glycopeptide antibacterials"	"tec,tei,teic,teicop,tp,tpl,tpn"	"NA"			0.4	"g"	"18989-4,25534-9,25535-6,34378-0,34379-8,4043-6,483-8,484-6,485-3,486-1,7051-6,80968-1"
 "TCM"		"Teicoplanin-macromethod"	"Glycopeptides"	"NA"			"NA"	"NA"					"NA"
-"TLV"	3081362	"Telavancin"	"Glycopeptides"	"J01XA03,QJ01XA03"	"Other antibacterials"	"Glycopeptide antibacterials"	"tela,telava"	"arbelic,nvancomycin,televancin"					"72894-9,73630-6,85051-1,88886-7"
-"TLT"	3002190	"Telithromycin"	"Macrolides/lincosamides"	"J01FA15,QJ01FA15"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"teli,telith"	"ketek,levviax"	0.8	"g"			"35843-2,35844-0,35845-7,41722-0"
-"TMX"	60021	"Temafloxacin"	"Fluoroquinolones"	"J01MA05,QJ01MA05"	"Quinolone antibacterials"	"Fluoroquinolones"	"tema,temafl"	"omniflox,temafloxacina,temafloxacine,temafloxacino,temafloxacinum"	0.8	"g"			"18990-2,487-9,488-7,489-5,490-3"
-"TEM"	171758	"Temocillin"	"Beta-lactams/penicillins"	"J01CA17,QJ01CA17"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"temo,temoci"	"negaban,temocilina,temocillina,temocilline,temocillinum"			4	"g"	"18991-0,491-1,492-9,493-7,494-5,54190-4"
-"TRB"	1549008	"Terbinafine"	"Antifungals/antimycotics"	"D01AE15,D01BA02,QD01AE15,QD01BA02"	"Antifungals for systemic use"	"Antifungals for systemic use"	"terb"	"afogan,bramazil,bramizil,corbinal,lamasil,lamisil,muzonal,shoprite,terbina,terbinafina,terbinafinum,terbine,terbinex,terbisil,zabel"	0.25	"g"			"10720-1,10721-9,18992-8"
-"TRC"	441383	"Terconazole"	"Antifungals/antimycotics"	"G01AG02,QG01AG02"			"NA"	"fungistat,panlomyc,terazol,terconazol,terconazolum,tercospor,tetrazol,triaconazole,zazole"					"55196-0"
+"TLV"	3081362	"Telavancin"	"Lipoglycopeptides,Glycopeptides"	"J01XA03,QJ01XA03"	"Other antibacterials"	"Glycopeptide antibacterials"	"tela,telava"	"arbelic,nvancomycin,televancin"					"72894-9,73630-6,85051-1,88886-7"
+"TLT"	3002190	"Telithromycin"	"Macrolides"	"J01FA15,QJ01FA15"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"teli,telith"	"ketek,levviax"	0.8	"g"			"35843-2,35844-0,35845-7,41722-0"
+"TMX"	60021	"Temafloxacin"	"Fluoroquinolones,Quinolones"	"J01MA05,QJ01MA05"	"Quinolone antibacterials"	"Fluoroquinolones"	"tema,temafl"	"omniflox,temafloxacina,temafloxacine,temafloxacino,temafloxacinum"	0.8	"g"			"18990-2,487-9,488-7,489-5,490-3"
+"TEM"	171758	"Temocillin"	"Penicillins,Beta-lactams"	"J01CA17,QJ01CA17"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"temo,temoci"	"negaban,temocilina,temocillina,temocilline,temocillinum"			4	"g"	"18991-0,491-1,492-9,493-7,494-5,54190-4"
+"TRB"	1549008	"Terbinafine"	"Antifungals"	"D01AE15,D01BA02,QD01AE15,QD01BA02"	"Antifungals for systemic use"	"Antifungals for systemic use"	"terb"	"afogan,bramazil,bramizil,corbinal,lamasil,lamisil,muzonal,shoprite,terbina,terbinafina,terbinafinum,terbine,terbinex,terbisil,zabel"	0.25	"g"			"10720-1,10721-9,18992-8"
+"TRC"	441383	"Terconazole"	"Antifungals"	"G01AG02,QG01AG02"			"NA"	"fungistat,panlomyc,terazol,terconazol,terconazolum,tercospor,tetrazol,triaconazole,zazole"					"55196-0"
 "TRZ"	65720	"Terizidone"	"Antimycobacterials"	"J04AK03,QJ04AK03"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"NA"	"terivalidin,terizidona,terizidonum"					"NA"
 "TCY"	54675776	"Tetracycline"	"Tetracyclines"	"A01AB13,D06AA04,J01AA07,QA01AB13,QD06AA04,QG01AA90,QG51AA02,QJ01AA07,QJ51AA07,QS01AA09,QS02AA08,QS03AA02,S01AA09,S02AA08,S03AA02"	"Tetracyclines"	"Tetracyclines"	"tc,te,tet,tetcyc,tetr,tetra"	"abramycin,abricycline,agromicina,ambramicina,ambramycin,biocycline,brodspec,cefracycline,centet,ciclibion,copharlan,criseociclina,democracin,deschlorobiomycin,economycin,hostacyclin,lexacycline,limecycline,liquamycin,mericycline,micycline,neocycline,omegamycin,orlycycline,panmycin,purocyclina,roviciclina,solvocin,tetrabon,tetraciclina,tetracyclinehydrate,tetracyclinum,tetracyn,tetradecin,tetrafil,tetraverine,tetrazyklin,tsiklomistsin,tsiklomitsin,veracin,vetacyclinum"	1	"g"	1	"g"	"101504-9,18993-6,25272-6,4045-1,495-2,496-0,497-8,498-6,7052-4,87590-6"
 "TCY-S"		"Tetracycline screening test"	"Tetracyclines"	"NA"			"tcy screen"	"NA"					"NA"
-"TOL"	54691494	"Tetracycline/oleandomycin"	"Other antibacterials"	"J01RA08,QJ01RA08"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
-"TET"	65450	"Tetroxoprim"	"Other antibacterials"	"NA"			"NA"	"primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex"					"NA"
+"TOL"	54691494	"Tetracycline/oleandomycin"	"Tetracyclines"	"J01RA08,QJ01RA08"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
+"TET"	65450	"Tetroxoprim"	"Other"	"NA"			"NA"	"primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex"					"NA"
 "THA"	9568512	"Thiacetazone"	"Oxazolidinones"	"NA"			"NA"	"acetanilide,aktivan,ambathizon,amitiozon,antib,benthiozone,benzothiozane,benzothiozon,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mivizon,myvizone,neotibil,neustab,novakol,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibon,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal,tubin"					"32384-0,54184-7,54204-3"
 "THI"	27200	"Thiamphenicol"	"Phenicols"	"J01BA02,QJ01BA02,QJ51BA02"	"Amphenicols"	"Amphenicols"	"thiaph"	"armai,dextrosulfenidol,dextrosulphenidol,igralin,racefenicol,racefenicolo,racefenicolum,raceophenidol,thiamphenicolum,thiocymetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamycine"	1.5	"g"	1.5	"g"	"41723-8,41724-6,41725-3,54169-8"
 "TAT"	9568512	"Thioacetazone"	"Antimycobacterials"	"J04AK07,QJ04AK07"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
 "THI1"		"Thioacetazone/isoniazid"	"Antimycobacterials"	"J04AM04,QJ04AM04"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
-"TIA"	656958	"Tiamulin"	"Other antibacterials"	"QJ01XQ01"			"tiamul"	"denagard,thiamutilin,tiamulina,tiamuline,tiamulinum"					"35846-5,35847-3,35848-1,87589-8"
-"TIC"	36921	"Ticarcillin"	"Beta-lactams/penicillins"	"J01CA13,QJ01CA13"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"tc,ti,tic,tica,ticarc"	"ticar,ticarcilina,ticarcilline,ticarcillinum,timentin"			15	"g"	"18994-4,18995-1,25254-4,4054-3,4055-0,499-4,500-9,501-7,502-5,503-3,504-1,505-8,506-6,55716-5,55717-3,55718-1,55719-9,7053-2,7054-0"
-"TCC"	6437075	"Ticarcillin/clavulanic acid"	"Beta-lactams/penicillins"	"J01CR03,QJ01CR03"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"t/c,tcc,ticcla,ticl,tim,tlc"	"augpenin"			15	"g"	"NA"
+"TIA"	656958	"Tiamulin"	"Other"	"QJ01XQ01"			"tiamul"	"denagard,thiamutilin,tiamulina,tiamuline,tiamulinum"					"35846-5,35847-3,35848-1,87589-8"
+"TIC"	36921	"Ticarcillin"	"Penicillins,Beta-lactams"	"J01CA13,QJ01CA13"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"tc,ti,tic,tica,ticarc"	"ticar,ticarcilina,ticarcilline,ticarcillinum,timentin"			15	"g"	"18994-4,18995-1,25254-4,4054-3,4055-0,499-4,500-9,501-7,502-5,503-3,504-1,505-8,506-6,55716-5,55717-3,55718-1,55719-9,7053-2,7054-0"
+"TCC"	6437075	"Ticarcillin/clavulanic acid"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"J01CR03,QJ01CR03"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"t/c,tcc,ticcla,ticl,tim,tlc"	"augpenin"			15	"g"	"NA"
 "TGC"	54686904	"Tigecycline"	"Tetracyclines"	"J01AA12,QJ01AA12"	"Tetracyclines"	"Tetracyclines"	"tgc,tig,tige,tigecy"	"tigeciclina,tigecyclin,tigecyclinehydrate,tigilcycline,tygacil"			0.1	"g"	"101499-2,42354-1,42355-8,42356-6,42357-4,55158-0"
-"TMN"		"Tigemonam"	"Monobactams"	"NA"			"NA"	"NA"					"NA"
-"TBQ"	65592	"Tilbroquinol"	"Fluoroquinolones"	"P01AA05"			"NA"	"tilbroquinolum"					"NA"
-"TIP"	24860548	"Tildipirosin"	"Macrolides/lincosamides"	"QJ01FA96"			"NA"	"zuprevo"					"100060-3,88375-1,88377-7"
-"TIL"	5282521	"Tilmicosin"	"Macrolides/lincosamides"	"QJ01FA91"			"tilmic"	"micotil,pulmotil,tilmicosina,tilmicosine,tilmicosinum,tilmovet"					"35849-9,35850-7,35851-5,87588-0"
-"TIN"	5479	"Tinidazole"	"Other antibacterials"	"G01AF21,J01XD02,P01AB02,QG01AF21,QJ01XD02,QP51AA02"	"Other antibacterials"	"Imidazole derivatives"	"tini"	"amtiba,bioshik,fasigin,fasigyn,glongyn,haisigyn,isotinidazole,pletil,protozol,simplotan,sorquetan,symplotan,tindamax,tindazole,tinidazolum,tricolam,trimonase"	2	"g"	1.5	"g"	"54928-7,55720-7,55721-5,55722-3"
+"TMN"		"Tigemonam"	"Monobactams,Beta-lactams"	"NA"			"NA"	"NA"					"NA"
+"TBQ"	65592	"Tilbroquinol"	"Fluoroquinolones,Quinolones"	"P01AA05"			"NA"	"tilbroquinolum"					"NA"
+"TIP"	24860548	"Tildipirosin"	"Macrolides"	"QJ01FA96"			"NA"	"zuprevo"					"100060-3,88375-1,88377-7"
+"TIL"	5282521	"Tilmicosin"	"Macrolides"	"QJ01FA91"			"tilmic"	"micotil,pulmotil,tilmicosina,tilmicosine,tilmicosinum,tilmovet"					"35849-9,35850-7,35851-5,87588-0"
+"TIN"	5479	"Tinidazole"	"Other"	"G01AF21,J01XD02,P01AB02,QG01AF21,QJ01XD02,QP51AA02"	"Other antibacterials"	"Imidazole derivatives"	"tini"	"amtiba,bioshik,fasigin,fasigyn,glongyn,haisigyn,isotinidazole,pletil,protozol,simplotan,sorquetan,symplotan,tindamax,tindazole,tinidazolum,tricolam,trimonase"	2	"g"	1.5	"g"	"54928-7,55720-7,55721-5,55722-3"
 "TCR"	3001386	"Tiocarlide"	"Antimycobacterials"	"J04AD02,QJ04AD02"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"NA"	"aethoksid,aethoxydum,amixyl,datanil,disocarban,disoxyl,ethoxide,etocarlid,etocarlida,etocarlide,etocarlidum,etoksid,thiocarlide,tiocarlid,tiocarlida,tiocarlidum"	7	"g"			"NA"
-"TDC"	10247721	"Tiodonium chloride"	"Other antibacterials"	"NA"			"NA"	"tiodonium"					"NA"
-"TXC"	65788	"Tioxacin"	"Fluoroquinolones"	"NA"			"NA"	"tioxacine,tioxacino,tioxacinum"					"NA"
-"TIZ"	394397	"Tizoxanide"	"Other antibacterials"	"NA"			"NA"	"NA"					"73585-2,73607-4,73629-8"
+"TDC"	10247721	"Tiodonium chloride"	"Other"	"NA"			"NA"	"tiodonium"					"NA"
+"TXC"	65788	"Tioxacin"	"Fluoroquinolones,Quinolones"	"NA"			"NA"	"tioxacine,tioxacino,tioxacinum"					"NA"
+"TIZ"	394397	"Tizoxanide"	"Other"	"NA"			"NA"	"NA"					"73585-2,73607-4,73629-8"
 "TOB"	36294	"Tobramycin"	"Aminoglycosides"	"J01GB01,QJ01GB01,QS01AA12,S01AA12"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"nn,tm,to,tob,tobr,tobram"	"aktob,bethkis,distobram,gotabiotic,kitabis,nebcin,nebicin,nebramycin,tenebrimycin,tenemycin,tobacin,tobracin,tobradex,tobradistin,tobralex,tobramaxin,tobramicin,tobramicina,tobramitsetin,tobramycetin,tobramycine,tobramycinum,tobrased,tobrex"			0.24	"g"	"101496-8,13584-8,17808-7,18996-9,22750-4,22751-2,22752-0,25227-0,25800-4,31094-6,31095-3,31096-1,35239-3,35670-9,4057-6,4058-4,4059-2,507-4,508-2,509-0,50927-3,510-8,52962-8,59380-6,7055-7,80966-5"
 "TOH"		"Tobramycin-high"	"Aminoglycosides"	"NA"			"tobra high,tobramycin high,tohl"	"NA"					"NA"
-"TFX"	5517	"Tosufloxacin"	"Fluoroquinolones"	"J01MA22,QJ01MA22,QS01AE09,S01AE09"			"tosufl"	"NA"	0.45	"g"			"100061-1,76146-0"
+"TFX"	5517	"Tosufloxacin"	"Fluoroquinolones,Quinolones"	"J01MA22,QJ01MA22,QS01AE09,S01AE09"			"tosufl"	"NA"	0.45	"g"			"100061-1,76146-0"
 "TMP"	5578	"Trimethoprim"	"Trimethoprims"	"J01EA01,QJ01EA01,QJ51EA01"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	"t,tmp,tr,tri,trim,w"	"abaprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacin,bacterial,bacticel,bactifor,bactoprim,bactramin,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,conprim,cotrimel,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,futin,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lastrim,lescot,monoprim,monotrim,monotrimin,novotrimel,omstat,pancidim,proloprim,protrin,purbal,resprim,roubac,roubal,salvatrim,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,trimethioprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexol,trimezol,trimogal,trimono,trimopan,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim"	0.4	"g"	0.4	"g"	"101495-0,11005-6,17747-7,18997-7,18998-5,20387-7,23614-1,23631-5,25273-4,32342-8,4079-0,4080-8,4081-6,511-6,512-4,513-2,514-0,515-7,516-5,517-3,518-1,55584-7,7056-5,7057-3,80552-3,80973-1"
-"SXT"	358641	"Trimethoprim/sulfamethoxazole"	"Trimethoprims"	"J01EE01"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"cot,cotrim,sxt,t/s,tms,trisul,trsu,trsx,ts"	"abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrizol,bactromin,bactropin,baktar,benzenesulfonamide,berlocid,bibacrim,biseptol,centran,centrin,chemitrim,chemotrim,ciplin,comox,cotribene,cotrim,cotrimhexal,cotrimoxazol,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,eslectin,esteprim,eusaprim,fectrim,gamazole,gantanol,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,insozalin,jenamoxazol,kemoprim,kepinol,laratrim,linaris,maxtrim,metoxal,microtrim,mikrosid,momentol,nopil,oecotrim,omsat,oriprim,oxaprim,pantoprim,potrox,primazole,radonil,septra,septrim,servitrim,sigaprim,sigaprin,sulfatrim,sulfotrim,sulfotrimin,sulmeprim,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,tribakin,trifen,trigonyl,trimedin,trimesulf,trimethoprimsulfa,trimetoger,trimexazol,trimezole,trimforte,trimosulfa,uroplus"					"101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3"
-"TRL"	202225	"Troleandomycin"	"Macrolides/lincosamides"	"J01FA08,QJ01FA08"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"NA"	"aovine,cyclamycin,evramicina,matromicina,oleandocetin,oleandocetine,tekmisin,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycine,troleandomycinum,viamicina,wytrion"	1	"g"			"18999-3,519-9,520-7,521-5,522-3"
-"TRO"	55886	"Trospectomycin"	"Other antibacterials"	"NA"			"trospe"	"trospectinomycin,trospectomicina,trospectomycine,trospectomycinum"					"NA"
-"TVA"	62959	"Trovafloxacin"	"Fluoroquinolones"	"J01MA13,QJ01MA13"	"Quinolone antibacterials"	"Fluoroquinolones"	"trov,trovaf"	"trovan,turvel"	0.2	"g"	0.2	"g"	"23642-2,23643-0,35855-6,7058-1"
-"TUL"	9832301	"Tulathromycin"	"Macrolides/lincosamides"	"QJ01FA94"			"tulath"	"arovyn,draxxin,increxxa,macrosyn,tulieve,tulissin"					"76149-4,87798-5"
-"TYL"	5280440	"Tylosin"	"Macrolides/lincosamides"	"QJ01FA90,QJ51FA90"			"tylo"	"fradizine,tilosina,tylan,tylocine,tylosine,tylosinum,vubityl"					"35856-4,35857-2,35858-0,87587-2"
-"TYL1"	6441094	"Tylvalosin"	"Macrolides/lincosamides"	"QJ01FA92"			"tvn"	"aivlosin"					"101526-2,87586-4"
-"PRU1"	124225	"Ulifloxacin (Prulifloxacin)"	"Other antibacterials"	"NA"			"NA"	"NA"					"NA"
+"SXT"	358641	"Trimethoprim/sulfamethoxazole"	"Trimethoprims,Sulfonamides"	"J01EE01"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"cot,cotrim,sxt,t/s,tms,trisul,trsu,trsx,ts"	"abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrizol,bactromin,bactropin,baktar,benzenesulfonamide,berlocid,bibacrim,biseptol,centran,centrin,chemitrim,chemotrim,ciplin,comox,cotribene,cotrim,cotrimhexal,cotrimoxazol,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,eslectin,esteprim,eusaprim,fectrim,gamazole,gantanol,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,insozalin,jenamoxazol,kemoprim,kepinol,laratrim,linaris,maxtrim,metoxal,microtrim,mikrosid,momentol,nopil,oecotrim,omsat,oriprim,oxaprim,pantoprim,potrox,primazole,radonil,septra,septrim,servitrim,sigaprim,sigaprin,sulfatrim,sulfotrim,sulfotrimin,sulmeprim,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,tribakin,trifen,trigonyl,trimedin,trimesulf,trimethoprimsulfa,trimetoger,trimexazol,trimezole,trimforte,trimosulfa,uroplus"					"101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3"
+"TRL"	202225	"Troleandomycin"	"Macrolides"	"J01FA08,QJ01FA08"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"NA"	"aovine,cyclamycin,evramicina,matromicina,oleandocetin,oleandocetine,tekmisin,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycine,troleandomycinum,viamicina,wytrion"	1	"g"			"18999-3,519-9,520-7,521-5,522-3"
+"TRO"	55886	"Trospectomycin"	"Other"	"NA"			"trospe"	"trospectinomycin,trospectomicina,trospectomycine,trospectomycinum"					"NA"
+"TVA"	62959	"Trovafloxacin"	"Fluoroquinolones,Quinolones"	"J01MA13,QJ01MA13"	"Quinolone antibacterials"	"Fluoroquinolones"	"trov,trovaf"	"trovan,turvel"	0.2	"g"	0.2	"g"	"23642-2,23643-0,35855-6,7058-1"
+"TUL"	9832301	"Tulathromycin"	"Macrolides"	"QJ01FA94"			"tulath"	"arovyn,draxxin,increxxa,macrosyn,tulieve,tulissin"					"76149-4,87798-5"
+"TYL"	5280440	"Tylosin"	"Macrolides"	"QJ01FA90,QJ51FA90"			"tylo"	"fradizine,tilosina,tylan,tylocine,tylosine,tylosinum,vubityl"					"35856-4,35857-2,35858-0,87587-2"
+"TYL1"	6441094	"Tylvalosin"	"Macrolides"	"QJ01FA92"			"tvn"	"aivlosin"					"101526-2,87586-4"
+"PRU1"	124225	"Ulifloxacin (Prulifloxacin)"	"Other"	"NA"			"NA"	"NA"					"NA"
 "VAN"	14969	"Vancomycin"	"Glycopeptides"	"A07AA09,J01XA01,QA07AA09,QJ01XA01,QS01AA28,S01AA28"	"Other antibacterials"	"Glycopeptide antibacterials"	"va,van,vanc,vancom"	"vancocin,vancoled,vancomicina,vancomycine,vancomycinum"	2	"g"	2	"g"	"13586-3,13587-1,19000-9,20578-1,23615-8,25228-8,31012-8,39092-2,39796-8,39797-6,4089-9,4090-7,4091-5,4092-3,50938-0,523-1,524-9,525-6,526-4,59381-4,7059-9,92241-9,97657-1"
 "VAM"		"Vancomycin-macromethod"	"Glycopeptides"	"NA"			"NA"	"NA"					"NA"
 "VIO"	135398671	"Viomycin"	"Antimycobacterials"	"NA"			"NA"	"florimycin,floromycin,vioactane,viocin,viomicin,viomicina,viomycine,viomycinum"					"19001-7,23616-6,527-2,528-0,529-8,530-6"
-"VIR"	11979535	"Virginiamycine"	"Other antibacterials"	"NA"			"NA"	"NA"					"NA"
-"VOR"	71616	"Voriconazole"	"Antifungals/antimycotics"	"J02AC03,QJ02AC03"	"Antimycotics for systemic use"	"Triazole derivatives"	"vori,vorico,vrc"	"vfend,voriconazol,voriconazolum,voriconzole,vorikonazole"	0.4	"g"	0.4	"g"	"32379-0,35862-2,35863-0,38370-3,41199-1,41200-7,53902-3,73676-9,80553-1,80651-3"
-"XBR"	72144	"Xibornol"	"Other antibacterials"	"J01XX02,QJ01XX02"	"Other antibacterials"	"Other antibacterials"	"NA"	"bactacine,bracen,nanbacine,xibornolo,xibornolum"					"NA"
-"ZID"	77846445	"Zidebactam"	"Other antibacterials"	"NA"			"NA"	"zidebactamsalt"					"NA"
-"ZFD"		"Zoliflodacin"		"NA"			"NA"	"NA"					"NA"
+"VIR"	11979535	"Virginiamycine"	"Other"	"NA"			"NA"	"NA"					"NA"
+"VOR"	71616	"Voriconazole"	"Antifungals"	"J02AC03,QJ02AC03"	"Antimycotics for systemic use"	"Triazole derivatives"	"vori,vorico,vrc"	"vfend,voriconazol,voriconazolum,voriconzole,vorikonazole"	0.4	"g"	0.4	"g"	"32379-0,35862-2,35863-0,38370-3,41199-1,41200-7,53902-3,73676-9,80553-1,80651-3"
+"XBR"	72144	"Xibornol"	"Other"	"J01XX02,QJ01XX02"	"Other antibacterials"	"Other antibacterials"	"NA"	"bactacine,bracen,nanbacine,xibornolo,xibornolum"					"NA"
+"ZID"	77846445	"Zidebactam"	"Beta-lactamase inhibitors"	"NA"			"NA"	"zidebactamsalt"					"NA"
+"ZFD"		"Zoliflodacin"	"Spiropyrimidinetriones"	"NA"			"zol"	"NA"					"NA"

data-raw/microorganisms.md5

@@ -1 +1 @@
-5908f9e6e7687dfb8301d27fb26d1790
+6dc4dded108052760bfb626df03435e2

data-raw/translations.tsv

@@ -1,8 +1,8 @@
 pattern	regular_expr	case_sensitive	affect_ab_name	affect_mo_name	en	ar	bn	zh	cs	da	nl	fi	fr	de	el	hi	id	it	ja	ko	no	pl	pt	ro	ru	es	sw	sv	tr	uk	ur	vi
 language name English	FALSE	FALSE	FALSE	FALSE	English	Arabic	Bengali	Chinese	Czech	Danish	Dutch	Finnish	French	German	Greek	Hindi	Indonesian	Italian	Japanese	Korean	Norwegian	Polish	Portuguese	Romanian	Russian	Spanish	Swahili	Swedish	Turkish	Ukrainian	Urdu	Vietnamese
 language name	FALSE	FALSE	FALSE	FALSE	English	العربية	ইংরেজি	汉语	Čeština	Dansk	Nederlands	Suomi	Français	Deutsch	Ελληνικά	हिन्दी	Inggris	Italiano	日本語	영어	Norsk	Polski	Português	Română	Русский	Español	Kiswahili	Svenska	Türkçe	Українська	انگریزی	Tiếng Anh
-Coagulase-negative Staphylococcus	TRUE	TRUE	FALSE	TRUE	Coagulase-negative Staphylococcus	المكورات العنقودية سالبة التخثر	কোয়াগুলেজ-নেগেটিভ স্ট্যাফিলোকক্কাস	凝固酶阴性葡萄球菌	Koaguláza-negativní stafylokok	Koagulase-negative stafylokokker	Coagulase-negatieve Staphylococcus	Koagulaasinegatiivinen stafylokokki	Staphylococcus à coagulase négative	Koagulase-negative Staphylococcus	Σταφυλόκοκκος με αρνητική πηκτικότητα	कोएगुलेज़-ऩेगेटिव स्टैफिलोकोकस	Stafilokokus koagulase-negatif	Staphylococcus negativo coagulasi	コアグラーゼ陰性ブドウ球菌	코아귤라제 음성 포도상구균	Koagulase-negative stafylokokker	Staphylococcus koagulazoujemny	Staphylococcus coagulase negativo	Stafilococ coagulazo-negativ	Коагулазоотрицательный стафилококк	Staphylococcus coagulasa negativo	Staphylococcus wasiokuwa na coagulase	Koagulasnegativa stafylokocker	Koagülaz-negatif Stafilokok	Коагулазонегативний стафілокок	کواگولیز منفی اسٹیفیلوکوکس	Staphylococcus âm tính với coagulase
-Coagulase-positive Staphylococcus	TRUE	TRUE	FALSE	TRUE	Coagulase-positive Staphylococcus	المكورات العنقودية موجبة التخثر	কোয়াগুলেজ-পজিটিভ স্ট্যাফিলোকক্কাস	凝固酶阳性葡萄球菌	Koagulázopozitivní stafylokok	Koagulase-positive stafylokokker	Coagulase-positieve Staphylococcus	Koagulaasipositiivinen stafylokokki	Staphylococcus à coagulase positif	Koagulase-positive Staphylococcus	Σταφυλόκοκκος θετικός στην πήξη	कोएगुलेज़-पॉज़िटिव स्टैफिलोकोकस	Stafilokokus koagulase-positif	Staphylococcus positivo coagulasi	コアグラーゼ陽性ブドウ球菌	코아귤라제 양성 포도상구균	Koagulase-positive stafylokokker	Staphylococcus koagulazo-dodatni	Staphylococcus coagulase positivo	Stafilococul coagulazo-pozitiv	Коагулазоположительный стафилококк	Staphylococcus coagulasa positivo	Staphylococcus wenye coagulase	Koagulaspositiva stafylokocker	Koagülaz-pozitif Stafilokok	Коагулазопозитивний стафілокок	کواگولیز مثبت اسٹیفیلوکوکس	Staphylococcus dương tính với coagulase
+Coagulase-negative Staphylococcus	TRUE	TRUE	FALSE	TRUE	Coagulase-negative Staphylococcus	المكورات العنقودية سالبة التخثر	কোয়াগুলেজ-নেগেটিভ স্ট্যাফিলোকক্কাস	凝固酶阴性葡萄球菌	Koaguláza-negativní stafylokok	Koagulase-negative stafylokokker	Coagulase-negatieve Staphylococcus	Koagulaasinegatiivinen stafylokokki	Staphylococcus à coagulase négative	Koagulase-negative Staphylococcus	Σταφυλόκοκκος με αρνητική πηκτικότητα	कोएगुलेज़-ऩेगेटिव स्टैफिलोकोकस	Stafilokokus koagulase-negatif	Stafilococco coagulasi-negativo	コアグラーゼ陰性ブドウ球菌	코아귤라제 음성 포도상구균	Koagulase-negative stafylokokker	Staphylococcus koagulazoujemny	Staphylococcus coagulase negativo	Stafilococ coagulazo-negativ	Коагулазоотрицательный стафилококк	Staphylococcus coagulasa negativo	Staphylococcus wasiokuwa na coagulase	Koagulasnegativa stafylokocker	Koagülaz-negatif Stafilokok	Коагулазонегативний стафілокок	کواگولیز منفی اسٹیفیلوکوکس	Staphylococcus âm tính với coagulase
+Coagulase-positive Staphylococcus	TRUE	TRUE	FALSE	TRUE	Coagulase-positive Staphylococcus	المكورات العنقودية موجبة التخثر	কোয়াগুলেজ-পজিটিভ স্ট্যাফিলোকক্কাস	凝固酶阳性葡萄球菌	Koagulázopozitivní stafylokok	Koagulase-positive stafylokokker	Coagulase-positieve Staphylococcus	Koagulaasipositiivinen stafylokokki	Staphylococcus à coagulase positif	Koagulase-positive Staphylococcus	Σταφυλόκοκκος θετικός στην πήξη	कोएगुलेज़-पॉज़िटिव स्टैफिलोकोकस	Stafilokokus koagulase-positif	Stafilococco coagulasi-positivo	コアグラーゼ陽性ブドウ球菌	코아귤라제 양성 포도상구균	Koagulase-positive stafylokokker	Staphylococcus koagulazo-dodatni	Staphylococcus coagulase positivo	Stafilococul coagulazo-pozitiv	Коагулазоположительный стафилококк	Staphylococcus coagulasa positivo	Staphylococcus wenye coagulase	Koagulaspositiva stafylokocker	Koagülaz-pozitif Stafilokok	Коагулазопозитивний стафілокок	کواگولیز مثبت اسٹیفیلوکوکس	Staphylococcus dương tính với coagulase
 Beta-haemolytic Streptococcus	TRUE	TRUE	FALSE	TRUE	Beta-haemolytic Streptococcus	العقديات الحالة للدم من النوع بيتا	বিটা-হেমোলাইটিক স্ট্রেপটোকক্কাস	β-溶血性链球菌	Beta-hemolytický streptokok	Beta-haemolytiske streptokokker	Beta-hemolytische Streptococcus	Beeta-hemolyyttinen streptokokki	Streptococcus Bêta-hémolytique	Beta-hämolytischer Streptococcus	Β-αιμολυτικός στρεπτόκοκκος	बीटा-हीमोलिटिक स्ट्रेप्टोकोकस	Streptokokus beta-hemolitik	Streptococcus Beta-emolitico	ベータ溶血性レンサ球菌	베타 용혈성 연쇄상구균	Beta-hemolytiske streptokokker	Streptococcus beta-hemolityczny	Streptococcus Beta-hemolítico	Streptococ beta-hemolitic	Бета-гемолитический стрептококк	Streptococcus Beta-hemolítico	Streptococcus wa beta-hemolitiki	Beta-hemolytiska streptokocker	Beta-hemolitik Streptokok	Бета-гемолітичний стрептокок	بیٹا ہیمولائٹک اسٹریپٹوکوکس	Streptococcus tan máu beta
 unknown Gram-negatives	TRUE	TRUE	FALSE	TRUE	unknown Gram-negatives	سالبة الجرام غير معروفة	অজানা গ্রাম-নেগেটিভ	不明革兰氏阴性菌	neznámé gramnegativní	ukendte Gram-negative	onbekende Gram-negatieven	tuntemattomat gramnegatiiviset	Gram négatifs inconnus	unbekannte Gramnegativen	άγνωστοι αρνητικοί κατά Gram	अज्ञात ग्राम-ऩेगेटिव्स	Gram negatif tidak diketahui	Gram negativi sconosciuti	不明なグラム陰性菌	알 수 없는 그람 음성균	ukjent Gram-negative	Nieznane bakterie Gram-ujemne	Gram negativos desconhecidos	Gram-negative necunoscute	неизвестные грамотрицательные	Gram negativos desconocidos	Gram hasi wasiojulikana	okända gramnegativa bakterier	bilinmeyen Gram-negatifler	невідомі грамнегативні	نامعلوم گرام منفی	Gram âm chưa xác định
 unknown Gram-positives	TRUE	TRUE	FALSE	TRUE	unknown Gram-positives	موجبة الجرام غير معروفة	অজানা গ্রাম-পজিটিভ	不明革兰氏阳性菌	neznámé grampozitivní	ukendte Gram-positive	onbekende Gram-positieven	tuntemattomat grampositiiviset	Gram positifs inconnus	unbekannte Grampositiven	άγνωστοι θετικοί κατά Gram	अज्ञात ग्राम-पॉज़िटिव्स	Gram positif tidak diketahui	Gram positivi sconosciuti	未知のグラム陽性菌	알 수 없는 그람 양성균	ukjent Gram-positive	Nieznane bakterie Gram-dodatnie	Gram positivos desconhecidos	Gram-pozitive necunoscute	неизвестные грамположительные	Gram positivos desconocidos	Gram chanya wasiojulikana	okända Gram-positiva	bilinmeyen Gram-pozitifler	невідомі грампозитивні	نامعلوم گرام مثبت	Gram dương chưa xác định
@@ -280,7 +280,8 @@ Antifungals	FALSE	TRUE	TRUE	FALSE	Antifungals	مضادات الفطريات	অ
 Antifungals/antimycotics	FALSE	TRUE	TRUE	FALSE	Antifungals/antimycotics	مضادات الفطريات/الفطريات المُمرِضة	অ্যান্টিফাঙ্গালস/অ্যান্টিমাইকোটিকস	抗真菌药/抗真菌药	Antimykotika/antimykotika	Antimykotika/antimykotika	Antifungica/antimycotica	Sienilääkkeet/antimykootit	Antifongiques/antimycotiques	Antimykotika/Antimykotika	Αντιμυκητιασικά/αντιμυκητιασικά	प्रतिफफूंद/प्रतिमाइकोटिक्स  	Antijamur/antimikotik	Antifungini/antimicotici	抗真菌剤／抗真菌剤	항진균제/항진균성약물	Soppdrepende midler/antimykotika	Środki przeciwgrzybicze/przeciwmikotyczne	Antifúngicos/antimicóticos	Antifungice/antimicrotice	Противогрибковые препараты/антимикотики	Antifúngicos/antimicóticos	Dawa za kuua kuvu/antimaikoti	Antimykotika/antimykotika	Antifungaller/antimikotikler	Протигрибкові засоби/антимікотики	فنگس/اینٹی مائیکوٹک	Thuốc chống nấm/kháng nấm
 Antimycobacterials	FALSE	TRUE	TRUE	FALSE	Antimycobacterials	مضادات الفطريات الحمضية المقاومة	অ্যান্টিমাইকোব্যাকটেরিয়ালস	抗霉菌素类	Antimykobakteriální látky	Antimycobakterier	Antimycobacteriele middelen	Antimykobakteerit	Antimycobactériens	Antimykobakterielle Mittel	Αντιμυκοβακτηριακά	प्रतिमाइकोबैक्टीरियल्स  	Antimikobakteri	Antimicobatterici	抗マイコバクテリア薬	항항산균제	Antimykobakterielle midler	Środki przeciwgrzybicze	Antimycobacterials	Antimicobacteriene	Антимикобактериальные препараты	Antimicrobianos	Dawa dhidi ya mykobakteria	Antimykobakterier	Antimikobakteriyeller	Засоби, що діють на мікобактерії	اینٹی مائیکوبیکٹیریل	Thuốc chống trực khuẩn kháng axit
 Beta-lactams/penicillins	FALSE	TRUE	TRUE	FALSE	Beta-lactams/penicillins	البيتا-لاكتامات/البنسلينات	বেটা-ল্যাকটামস/পেনিসিলিনস	β-内酰胺类/青霉素类	Beta-laktamy/peniciliny	Beta-lactamer/penicilliner	Beta-lactams/penicillines	Beetalaktaamit/penisilliinit	Bêta-lactamines/pénicillines	Beta-Lactame/Penicilline	Β-λακτάμες/πενικιλλίνες	बीटा-लैक्टाम्स/पेनिसिलिन्स  	Beta-laktam/penisilin	Beta-lattami/penicilline	β-ラクタム系／ペニシリン系抗菌薬	베타-락탐/페니실린	Betalaktamer/penicilliner	Beta-laktamy/penicyliny	Beta-lactâmicas/penicilinas	Beta-lactame/peniciline	Бета-лактамы/пенициллины	Beta-lactámicos/penicilinas	Betalaktamu/penisilini	Beta-laktamer/penicilliner	Beta-laktamlar/penisilinler	Бета-лактами/пеніциліни	بیٹا لیکٹمز/پینسلنز	Beta-lactam/penicillin
-Betalactams	FALSE	TRUE	TRUE	FALSE	Betalactams	البيتا-لاكتامات	বেটা-ল্যাকটামস	β-内酰胺类	Beta-laktamy	Beta-lactamer	Beta-lactams	Beetalaktaamit	Bêta-lactamines	Beta-Lactame	Β-λακτάμες	बीटा-लैक्टाम्स	Beta-laktam	Beta-lattami	β-ラクタム系抗菌薬	베타-락탐	Betalaktamer	Beta-laktamy	Beta-lactâmicas	Beta-lactame	Бета-лактамы	Beta-lactámicos	Betalaktamu	Betalaktamer	Beta-laktamlar	Бета-лактами	بیٹا لیکٹمز	Beta-lactam
+Beta-lactams	FALSE	TRUE	TRUE	FALSE	Betalactams	البيتا-لاكتامات	বেটা-ল্যাকটামস	β-内酰胺类	Beta-laktamy	Beta-lactamer	Beta-lactams	Beetalaktaamit	Bêta-lactamines	Beta-Lactame	Β-λακτάμες	बीटा-लैक्टाम्स	Beta-laktam	Beta-lattami	β-ラクタム系抗菌薬	베타-락탐	Betalaktamer	Beta-laktamy	Beta-lactâmicas	Beta-lactame	Бета-лактамы	Beta-lactámicos	Betalaktamu	Betalaktamer	Beta-laktamlar	Бета-лактами	بیٹا لیکٹمز	Beta-lactam
+Beta-lactamase inhibitors	FALSE	TRUE	TRUE	FALSE	Beta-lactamase inhibitors	مثبطات بيتا-لاكتاماز	বেটা-ল্যাকটামেজ ইনহিবিটরস	β-内酰胺酶抑制剂	Inhibitory beta-laktamázy	Beta-laktamasehæmmere	Beta-lactamaseremmers	Beetalaktamaasin estäjät	Inhibiteurs de bêta-lactamase	Beta-Laktamase-Inhibitoren	Αναστολείς β-λακταμάσης	बीटा-लैक्टामेज़ अवरोधक	Inhibitor beta-laktamase	Inibitori delle beta-lattamasi	β-ラクタマーゼ阻害薬	베타-락타마제 억제제	Beta-laktamasehemmere	Inhibitory beta-laktamaz	Inibidores da beta-lactamase	Inhibitori de beta-lactamază	Ингибиторы бета-лактамаз	Inhibidores de beta-lactamasa	Vizuizi vya beta-laktamasi	Beta-laktamashämmare	Beta-laktamaz inhibitörleri	Інгібітори бета-лактамаз	بیٹا لیکٹامیز انہیبیٹرز	Chất ức chế beta-lactamase
 Carbapenems	FALSE	TRUE	TRUE	FALSE	Carbapenems	الكاربابينيمات	কার্বাপেনেমস	碳青霉烯类	Karbapenemy	Carbapenemer	Carbapenems	Karbapeneemit	Carbapénèmes	Carbapeneme	Καρβαπενέμες	कार्बापेनेम्स	Karbapenem	Carbapenemi	カルバペネム系抗生物質	카르바페넴	Carbapenemer	Karbapenemy	Carbapenêmicos	Carbapeneme	Карбапенемы	Carbapenémicos	Karbapenemu	Carbapenemer	Karbapenemler	Карбапенеми	کارباپینیمز	Carbapenem
 Cephalosporins	FALSE	TRUE	TRUE	FALSE	Cephalosporins	السيفالوسبورينات	সেফালোসপরিনস	头孢菌素类	Cefalosporiny	Cefalosporiner	Cefalosporines	Kefalosporiinit	Céphalosporines	Cephalosporine	Κεφαλοσπορίνες	सेफालोस्पोरिन्स  	Sefalosporin	Cefalosporine	セファロスポリン	세팔로스포린	Cefalosporiner	Cefalosporyny	Cefalosporinas	Cefalosporine	Цефалоспорины	Cefalosporinas	Sefalosporini	Kefalosporiner	Sefalosporinler	Цефалоспорини	سیفالوسپورنز	Cephalosporin
 Cephalosporins (1st gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporins (1st gen.)	السيفالوسبورينات (الجيل الأول)	সেফালোসপরিনস (১ম প্রজন্ম)	头孢菌素类（第一代）	Cefalosporiny (1. gen.)	Cefalosporiner (1. gen.)	Cefalosporines (1e gen.)	Kefalosporiinit (1. suk.)	Céphalosporines (1ère génération)	Cephalosporine (1. Gen.)	Κεφαλοσπορίνες (1ου γένους)	सेफालोस्पोरिन्स (प्रथम पीढ़ी)  	Sefalosporin (generasi 1)	Cefalosporine (1° gen.)	セファロスポリン系抗生物質（第1世代）	세팔로스포린 (1세대)	Cefalosporiner (1. generasjon)	Cefalosporyny (1. gen.)	Cefalosporinas (1º género)	Cefalosporine (prima generație)	Цефалоспорины (1-го пок.)	Cefalosporinas (1er gen.)	Sefalosporini (kizazi cha 1)	Kefalosporiner (första gen.)	Sefalosporinler (1. kuşak)	Цефалоспорини (1 пок.)	سیفالوسپورنز (پہلی نسل)	Cephalosporin (thế hệ 1)
@@ -302,6 +303,7 @@ Other antibacterials	FALSE	TRUE	TRUE	FALSE	Other antibacterials	مضادات ب
 Oxazolidinones	FALSE	TRUE	TRUE	FALSE	Oxazolidinones	الأوكسازوليدينونات	অক্সাজোলিডিনোনস	恶唑烷酮类	Oxazolidinone	Oxazolidinones	Oxazolidinonen	Oxazolidinonit	Oxazolidinones	Oxazolidinone	Οξαζολιδινόνες	ऑक्साज़ोलिडिनोन्स  	Oksazolidinon	Oxazolidinonas	オキサゾリジノン	옥사졸리디논	Oxazolidinones	Oksazolidynony	Oxazolidinonas	Oxazolidinone	Оксазолидиноны	Oxazolidinonas	Oxazolidinoni	Oxazolidinones	Oxazolidinonlar	Оксазолідинони	اوکسا زولڈی نونز	Oxazolidinone
 Penicillins	FALSE	TRUE	TRUE	FALSE	Penicillins	البنسلينات	পেনিসিলিনস	青霉素类	Пенициллины	Penicillins	Penicillines	Penisilliinit	Pénicillines	Penicillins	Πενικιλίνες	पेनिसिलिन्स  	Penisilin	Penicilinas	ペニシリン	페니실린	Penicillins	Penicyliny	Penicilinas	Peniciline	Пенициллины	Penicilinas	Penisilini	Penicillins	Penisilinler	Пеніциліни	پینسلن	Penicillin
 Phenicols	FALSE	TRUE	TRUE	FALSE	Phenicols	الفينيكولات	ফেনিকলস	酚类抗生素	Phenikoly	Fenicoler	Fenicols	Fenikolit	Phénicols	Phenicol	Φαινικόλες	फेनिकोल्स	Fenikol	Fenicoli	フェニコール	페니콜	Fenicoler	Fenikole	Fenicóis	Fenicoli	Фениколы	Fenicoles	Fenikoli	Fenicoler	Fenikoller	Фенікони	فینیکولز	Phenicols
+Phosphonics	FALSE	TRUE	TRUE	FALSE	Phosphonics	الفوسفونيّات	ফসফোনিকস	膦酸类	Phosphonáty	Fosfonater	Fosfonaten	Fosfonaatit	Phosphoniques	Phosphonates	Φωσφονικά	फॉस्फ़ोनिक्स	Fosfonik	Fosfonici	ホスホン酸系抗菌薬	포스포닉계	Fosfonater	Fosfoniany	Fosfônicos	Fosfonați	Фосфоники	Fosfónicos	Fosfoniki	Fosfonater	Fosfonikler	Фосфоніки	فاسفونکس	Các hợp chất phosphonic
 Polymyxins	FALSE	TRUE	TRUE	FALSE	Polymyxins	البوليميكسينات	পলিমিক্সিনস	多粘菌素类	Polymyxiny	Polymyxiner	Polymyxines	Polymysiinit	Polymyxines	Polymyxine	Πολυμυξίνες	पॉलीमिक्सिन्स  	Polimiksin	Polimixine	ポリミキシン	폴리믹신	Polymyxiner	Polimyksyny	Polimixinas	Polimixine	Полимиксины	Polimixinas	Polimiksini	Polymyxiner	Polimiksinler	Поліміксини	پولی مائکسینز	Polymyxin
 Quinolones	FALSE	TRUE	TRUE	FALSE	Quinolones	الكوينولونات	কুইনোলোনস	喹诺酮类	Chinolony	Kinoloner	Quinolonen	Kinolonit	Quinolones	Quinolone	Κινολόνες	क्विनोलोन्स  	Kuinalon	Chinoloni	キノロン	퀴놀론	Kinoloner	Quinolony	Quinolones	Quinolone	Хинолоны	Quinolonas	Kinoloni	Kinoloner	Kinolonlar	Хінолони	کوئنولونز	Quinolone
 Rifamycins	FALSE	TRUE	TRUE	FALSE	Rifamycins	الريفاميسينات	রিফামাইসিনস	利福霉素类	Rifamycine	Rifamycins	Rifamycinen	Rifamysiinit	Rifamycines	Rifamycine	Ριφαμυκίνες	रिफामाइसिन्स  	Rifamisin	Rifamicinas	リファマイシン	리팜이신	Rifamycins	Rifamycyny	Rifamycinas	Rifamicine	Рифамицины	Rifamicinas	Rifamasini	Rifamycins	Rifamisinler	Рифаміцини	ریفامائسنز	Rifamycin

man/AMR-options.Rd

@@ -4,18 +4,27 @@
 \alias{AMR-options}
 \title{Options for the AMR package}
 \description{
-This is an overview of all the package-specific \code{\link[=options]{options()}} you can set in the \code{AMR} package.
+This is an overview of all the package-specific options you can set in the \code{AMR} package. Set them using the \code{\link[=options]{options()}} function, e.g.:
+
+\code{options(AMR_guideline = "CLSI")}
 }
-\section{Options}{
+\section{Options (alphabetical order)}{
 
 \itemize{
 \item \code{AMR_antibiogram_formatting_type} \cr A \link{numeric} (1-22) to use in \code{\link[=antibiogram]{antibiogram()}}, to indicate which formatting type to use.
 \item \code{AMR_breakpoint_type} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".
-\item \code{AMR_capped_mic_handling} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate how capped MIC values (\code{<}, \code{<=}, \code{>}, \code{>=}) should be interpreted. Must be one of \code{"standard"}, \code{"strict"}, \code{"relaxed"}, or \code{"inverse"} - the default is \code{"standard"}.
+\item \code{AMR_capped_mic_handling} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate how capped MIC values (\code{<}, \code{<=}, \code{>}, \code{>=}) should be interpreted. Must be one of \code{"none"}, \code{"conservative"}, \code{"standard"}, or \code{"lenient"} - the default is \code{"conservative"}.
 \item \code{AMR_cleaning_regex} \cr A \link[base:regex]{regular expression} (case-insensitive) to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to clean the user input. The default is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar".
 \item \code{AMR_custom_ab} \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
 \item \code{AMR_custom_mo} \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
 \item \code{AMR_eucastrules} \cr A \link{character} to set the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
+\item \code{AMR_guideline} \cr A \link{character} to set the default guideline used throughout the \code{AMR} package wherever a \code{guideline} argument is available. This option is used as the default in e.g. \code{\link[=as.sir]{as.sir()}}, \code{\link[=resistance]{resistance()}}, \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=interpretive_rules]{interpretive_rules()}} and many plotting functions. \strong{While unset}, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).
+\itemize{
+\item For \code{\link[=as.sir]{as.sir()}}, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., \code{"CLSI"} or \code{"EUCAST"}) or the name including a year (e.g., \code{"CLSI 2019"}). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025.
+\item For \code{\link[=resistance]{resistance()}} and \code{\link[=susceptibility]{susceptibility()}}, this setting determines how the \code{"I"} (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, \code{"I"} is considered \emph{resistant} in susceptibility calculations; under EUCAST, \code{"I"} is considered \emph{susceptible} in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
+\item For \code{\link[=interpretive_rules]{interpretive_rules()}}, this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.
+\item For many plotting functions (e.g., for MIC or disk diffusion values), supplying \code{mo} and \code{ab} enables automatic SIR-based interpretative colouring. These colours are derived from \code{\link[=as.sir]{as.sir()}} in the background and therefore depend on the active \code{guideline} setting, which again uses EUCAST 2025 if not set explicitly.
+}
 \item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2025"}. Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).
 \item \code{AMR_ignore_pattern} \cr A \link[base:regex]{regular expression} to ignore (i.e., make \code{NA}) any match given in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions.
 \item \code{AMR_include_PKPD} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}.
@@ -43,7 +52,7 @@ In this file, you can set options such as...
 ...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with \code{\link[=as.sir]{as.sir()}}.
 \subsection{Share Options Within Team}{
 
-For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
+For a more collaborative approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
 \enumerate{
 \item Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
 \item For each user, open the \code{.Rprofile} file using \code{utils::file.edit("~/.Rprofile")} and put in there:

man/AMR.Rd

@@ -83,10 +83,10 @@ Other contributors:
   \item Judith M. Fonville [contributor]
   \item Kathryn Holt (\href{https://orcid.org/0000-0003-3949-2471}{ORCID}) [contributor]
   \item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
-  \item Matthew Saab [contributor]
+  \item Matthew Saab (\href{https://orcid.org/0009-0008-6626-7919}{ORCID}) [contributor]
   \item Natacha Couto (\href{https://orcid.org/0000-0002-9152-5464}{ORCID}) [contributor]
   \item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
-  \item Rogier P. Schade [contributor]
+  \item Rogier P. Schade (\href{https://orcid.org/0000-0002-9487-4467}{ORCID}) [contributor]
   \item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
   \item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]
   \item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]

man/ab_property.Rd

@@ -27,7 +27,7 @@ ab_synonyms(x, ...)
 
 ab_tradenames(x, ...)
 
-ab_group(x, language = get_AMR_locale(), ...)
+ab_group(x, language = get_AMR_locale(), all_groups = FALSE, ...)
 
 ab_atc(x, only_first = FALSE, ...)
 
@@ -59,6 +59,8 @@ set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
 
 \item{...}{In case of \code{\link[=set_ab_names]{set_ab_names()}} and \code{data} is a \link{data.frame}: columns to select (supports tidy selection such as \code{column1:column4}), otherwise other arguments passed on to \code{\link[=as.ab]{as.ab()}}.}
 
+\item{all_groups}{A \link{logical} to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting \code{all_groups = TRUE} would return all three for such an antibiotic, while \code{all_groups = FALSE} (default) only returns the most distinctive group name.}
+
 \item{only_first}{A \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group).}
 
 \item{administration}{Way of administration, either \code{"oral"} or \code{"iv"}.}
@@ -94,7 +96,7 @@ The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column ren
 
 World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 
-European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
+European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
 }
 
 \section{Download Our Reference Data}{

man/amr-tidymodels.Rd

@@ -2,21 +2,27 @@
 % Please edit documentation in R/tidymodels.R
 \name{amr-tidymodels}
 \alias{amr-tidymodels}
-\alias{all_mic}
-\alias{all_mic_predictors}
 \alias{all_sir}
 \alias{all_sir_predictors}
+\alias{all_mic}
+\alias{all_mic_predictors}
+\alias{all_disk}
+\alias{all_disk_predictors}
 \alias{step_mic_log2}
 \alias{step_sir_numeric}
 \title{AMR Extensions for Tidymodels}
 \usage{
+all_sir()
+
+all_sir_predictors()
+
 all_mic()
 
 all_mic_predictors()
 
-all_sir()
+all_disk()
 
-all_sir_predictors()
+all_disk_predictors()
 
 step_mic_log2(recipe, ..., role = NA, trained = FALSE, columns = NULL,
   skip = FALSE, id = recipes::rand_id("mic_log2"))
@@ -45,21 +51,22 @@ may affect the computations for subsequent operations.}
 \item{id}{A character string that is unique to this step to identify it.}
 }
 \description{
-This family of functions allows using AMR-specific data types such as \verb{<mic>} and \verb{<sir>} inside \code{tidymodels} pipelines.
+This family of functions allows using AMR-specific data types such as \verb{<sir>} and \verb{<mic>} inside \code{tidymodels} pipelines.
 }
 \details{
 You can read more in our online \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{AMR with tidymodels introduction}.
 
 Tidyselect helpers include:
 \itemize{
-\item \code{\link[=all_mic]{all_mic()}} and \code{\link[=all_mic_predictors]{all_mic_predictors()}} to select \verb{<mic>} columns
-\item \code{\link[=all_sir]{all_sir()}} and \code{\link[=all_sir_predictors]{all_sir_predictors()}} to select \verb{<sir>} columns
+\item \code{\link[=all_sir]{all_sir()}} and \code{\link[=all_sir_predictors]{all_sir_predictors()}} to select \code{\link[=as.sir]{<sir>}} columns
+\item \code{\link[=all_mic]{all_mic()}} and \code{\link[=all_mic_predictors]{all_mic_predictors()}} to select \code{\link[=as.mic]{<mic>}} columns
+\item \code{\link[=all_disk]{all_disk()}} and \code{\link[=all_disk_predictors]{all_disk_predictors()}} to select \code{\link[=as.disk]{<disk>}} columns
 }
 
 Pre-processing pipeline steps include:
 \itemize{
-\item \code{\link[=step_mic_log2]{step_mic_log2()}} to convert MIC columns to numeric (via \code{as.numeric()}) and apply a log2 transform, to be used with \code{\link[=all_mic_predictors]{all_mic_predictors()}}
 \item \code{\link[=step_sir_numeric]{step_sir_numeric()}} to convert SIR columns to numeric (via \code{as.numeric()}), to be used with \code{\link[=all_sir_predictors]{all_sir_predictors()}}: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA}. Keep this in mind for further processing, especially if the model does not allow for \code{NA} values.
+\item \code{\link[=step_mic_log2]{step_mic_log2()}} to convert MIC columns to numeric (via \code{as.numeric()}) and apply a log2 transform, to be used with \code{\link[=all_mic_predictors]{all_mic_predictors()}}
 }
 
 These steps integrate with \code{recipes::recipe()} and work like standard preprocessing steps. They are useful for preparing data for modelling, especially with classification models.
@@ -112,7 +119,13 @@ if (require("tidymodels")) {
     bind_cols(out_testing)
 
   # Evaluate predictions using standard classification metrics
-  our_metrics <- metric_set(accuracy, kap, ppv, npv)
+  our_metrics <- metric_set(accuracy,
+                            recall,
+                            precision,
+                            sensitivity,
+                            specificity,
+                            ppv,
+                            npv)
   metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
 
   # Show performance
@@ -120,6 +133,6 @@ if (require("tidymodels")) {
 }
 }
 \seealso{
-\code{\link[recipes:recipe]{recipes::recipe()}}, \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.sir]{as.sir()}}
+\code{\link[recipes:recipe]{recipes::recipe()}}, \code{\link[=as.sir]{as.sir()}}, \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}}
 }
 \keyword{internal}

man/antibiogram.Rd

@@ -72,7 +72,7 @@ retrieve_wisca_parameters(wisca_model, ...)
 
 \item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be \code{NULL} to not transform the input.}
 
-\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case_when]{case_when()}}. See \emph{Examples}.}
+\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case-and-replace-when]{case_when()}}. See \emph{Examples}.}
 
 \item{add_total_n}{\emph{(deprecated in favour of \code{formatting_type})} A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
 

man/antimicrobial_selectors.Rd

@@ -26,9 +26,11 @@
 \alias{oxazolidinones}
 \alias{penicillins}
 \alias{phenicols}
+\alias{phosphonics}
 \alias{polymyxins}
 \alias{quinolones}
 \alias{rifamycins}
+\alias{spiropyrimidinetriones}
 \alias{streptogramins}
 \alias{sulfonamides}
 \alias{tetracyclines}
@@ -98,6 +100,8 @@ penicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
 
 phenicols(only_sir_columns = FALSE, return_all = TRUE, ...)
 
+phosphonics(only_sir_columns = FALSE, return_all = TRUE, ...)
+
 polymyxins(only_sir_columns = FALSE, only_treatable = TRUE,
   return_all = TRUE, ...)
 
@@ -106,6 +110,8 @@ quinolones(only_sir_columns = FALSE, only_treatable = TRUE,
 
 rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)
 
+spiropyrimidinetriones(only_sir_columns = FALSE, return_all = TRUE, ...)
+
 streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)
 
 sulfonamides(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -173,42 +179,44 @@ The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[
 
 The \code{\link[=amr_selector]{amr_selector()}} function can be used to internally filter the \link{antimicrobials} data set on any results, see \emph{Examples}. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
 
-The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
+The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
 }
 \section{Full list of supported (antimicrobial) classes}{
 
 \itemize{
 \item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)
-\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP)
+\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), and ampicillin (AMP)
 \item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)
-\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
-\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)
-\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
-\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)
-\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
+\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
+\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), taniborbactam (TAN), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)
+\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
+\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), taniborbactam (TAN), and tebipenem (TBP)
+\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
 \item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)
 \item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), and loracarbef (LOR)
 \item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)
-\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)
+\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)
 \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)
 \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
 \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)
 \item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)
-\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), lincomycin (LIN), and pirlimycin (PRL)
+\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)
 \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)
-\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)
+\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), clindamycin inducible screening test (CLI-S), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)
 \item \code{\link[=monobactams]{monobactams()}} can select: \cr aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), carumonam (CAR), and tigemonam (TMN)
 \item \code{\link[=nitrofurans]{nitrofurans()}} can select: \cr furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin (NIT), and nitrofurazone (NIZ)
 \item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA)
 \item \code{\link[=penicillins]{penicillins()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)
 \item \code{\link[=phenicols]{phenicols()}} can select: \cr chloramphenicol (CHL), florfenicol (FLR), and thiamphenicol (THI)
+\item \code{\link[=phosphonics]{phosphonics()}} can select: \cr amikacin/fosfomycin (AKF) and fosfomycin (FOS)
 \item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)
-\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
+\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), oxolinic acid (OXO), ozenoxacin (OZN), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
 \item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)
+\item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin (ZFD)
 \item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
-\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), and sulfathiourea (SLF13)
-\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), and tigecycline (TGC)
-\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)
+\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfachlorpyridazine (SUP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethazine (SUM), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfasuccinamide (SNA), sulfathiazole (SUT), sulfathiourea (SLF13), sulfisoxazole (SOX), sulfonamide (SSS), and trimethoprim/sulfamethoxazole (SXT)
+\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), tetracycline/oleandomycin (TOL), and tigecycline (TGC)
+\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), iclaprim (ICL), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)
 \item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP)
 }
 }

man/antimicrobials.Rd

@@ -5,14 +5,14 @@
 \alias{antimicrobials}
 \alias{antibiotics}
 \alias{antivirals}
-\title{Data Sets with 617 Antimicrobial Drugs}
+\title{Data Sets with 618 Antimicrobial Drugs}
 \format{
-\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 497 observations and 14 variables:}{
+\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 498 observations and 14 variables:}{
 \itemize{
 \item \code{ab}\cr antimicrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
 \item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
 \item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{\strong{This is a unique identifier.}}
-\item \code{group}\cr A short and concise group name, based on WHONET and WHOCC definitions
+\item \code{group}\cr One or more short and concise group names, based on WHONET and WHOCC definitions
 \item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02} (last updated May 4th, 2025):
 \item \code{atc_group1}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like \code{"Macrolides, lincosamides and streptogramins"}
 \item \code{atc_group2}\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"}
@@ -50,7 +50,7 @@ LOINC:
 }
 }
 
-An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 497 rows and 14 columns.
+An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 498 rows and 14 columns.
 
 An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
 }

man/as.ab.Rd

@@ -52,7 +52,7 @@ You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab(
 
 World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 
-European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
+European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
 }
 
 \section{WHOCC}{

man/as.av.Rd

@@ -44,7 +44,7 @@ Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} fun
 
 World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 
-European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
+European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
 }
 
 \section{WHOCC}{

man/as.mic.Rd

@@ -12,13 +12,15 @@
 \alias{droplevels.mic}
 \title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
 \usage{
-as.mic(x, na.rm = FALSE, keep_operators = "all")
+as.mic(x, na.rm = FALSE, keep_operators = "all",
+  round_to_next_log2 = FALSE)
 
 is.mic(x)
 
 NA_mic_
 
-rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
+rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE,
+  round_to_next_log2 = FALSE)
 
 mic_p50(x, na.rm = FALSE, ...)
 
@@ -33,6 +35,8 @@ mic_p90(x, na.rm = FALSE, ...)
 
 \item{keep_operators}{A \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
 
+\item{round_to_next_log2}{A \link{logical} to round up all values to the next log2 level, that are not either 0.0001, 0.0002, 0.0005, 0.001, 0.002, 0.004, 0.008, 0.016, 0.032, 0.064, 0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, or 4096. Values that are already in this list (with or without operators), are left unchanged (including any operators).}
+
 \item{mic_range}{A manual range to rescale the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent rescaling on one side, e.g., \code{mic_range = c(NA, 32)}.}
 
 \item{as.mic}{A \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{TRUE} for \code{\link[=rescale_mic]{rescale_mic()}} and \code{FALSE} for \code{\link[=droplevels]{droplevels()}}. When setting this to \code{FALSE} in \code{\link[=rescale_mic]{rescale_mic()}}, the output will have factor levels that acknowledge \code{mic_range}.}

man/as.sir.Rd

@@ -19,7 +19,7 @@ For interpretations of minimum inhibitory concentration (MIC) values and disk di
 \item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
 \item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
 \item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
-\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
+\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/}.
 \item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2025, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
 }
 }
@@ -32,12 +32,15 @@ is.sir(x)
 
 is_sir_eligible(x, threshold = 0.05)
 
-\method{as.sir}{default}(x, S = "^(S|U)+$", I = "^(I)+$", R = "^(R)+$",
-  NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = interactive(), ...)
+\method{as.sir}{default}(x, S = "^(S|U|1)+$", I = "^(I|2)+$",
+  R = "^(R|3)+$", NI = "^(N|NI|V|4)+$", SDD = "^(SDD|D|H|5)+$",
+  WT = "^(WT|6)+$", NWT = "^(NWT|7)+$", NS = "^(NS|8)+$",
+  info = interactive(), ...)
 
 \method{as.sir}{mic}(x, mo = NULL, ab = deparse(substitute(x)),
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
   capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
+  as_wt_nwt = identical(breakpoint_type, "ECOFF"),
   add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
   substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
@@ -49,6 +52,7 @@ is_sir_eligible(x, threshold = 0.05)
 
 \method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
+  as_wt_nwt = identical(breakpoint_type, "ECOFF"),
   add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
   substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
@@ -61,6 +65,7 @@ is_sir_eligible(x, threshold = 0.05)
 \method{as.sir}{data.frame}(x, ..., col_mo = NULL,
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
   capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
+  as_wt_nwt = identical(breakpoint_type, "ECOFF"),
   add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
   substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
@@ -75,13 +80,13 @@ sir_interpretation_history(clean = FALSE)
 \arguments{
 \item{x}{Vector of values (for class \code{\link{mic}}: MIC values in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres).}
 
-\item{...}{For using on a \link{data.frame}: selection of columns to apply \code{as.sir()} to. Supports \link[tidyselect:starts_with]{tidyselect language} such as \code{where(is.mic)}, \code{starts_with(...)}, or \code{column1:column4}, and can thus also be \link[=amr_selector]{antimicrobial selectors} such as \code{as.sir(df, penicillins())}.
+\item{...}{For using on a \link{data.frame}: selection of columns to apply \code{as.sir()} to. Supports \link[tidyselect:starts_with]{tidyselect language} such as \code{where(is.mic)}, \code{starts_with(...)}, or \code{column1:column4}, and can thus also be \link[=amr_selector]{antimicrobial selectors}, e.g. \code{as.sir(df, penicillins())}.
 
 Otherwise: arguments passed on to methods.}
 
 \item{threshold}{Maximum fraction of invalid antimicrobial interpretations of \code{x}, see \emph{Examples}.}
 
-\item{S, I, R, NI, SDD}{A case-independent \link[base:regex]{regular expression} to translate input to this result. This regular expression will be run \emph{after} all non-letters and whitespaces are removed from the input.}
+\item{S, I, R, NI, SDD, WT, NWT, NS}{A case-independent \link[base:regex]{regular expression} to translate input to this result. This regular expression will be run \emph{after} all non-letters and whitespaces are removed from the input.}
 
 \item{info}{A \link{logical} to print information about the process, defaults to \code{TRUE} only in \link[base:interactive]{interactive sessions}.}
 
@@ -97,31 +102,33 @@ Otherwise: arguments passed on to methods.}
 
 \code{"none"}
 \itemize{
-\item \code{<=} and \code{>=} are treated as-is.
-\item \code{<} and \code{>} are treated as-is.
+\item \code{<=}, \code{<}, \code{>} and \code{>=} are ignored.
 }
 
-\code{"conservative"}
+\code{"conservative"} (default)
 \itemize{
-\item \code{<=} and \code{>=} return \code{"NI"} (non-interpretable) if the MIC is within the breakpoint guideline range.
-\item \code{<} always returns \code{"S"}, and \code{>} always returns \code{"R"}.
+\item \code{<=}, \code{<}, \code{>} and \code{>=} return \code{"NI"} (non-interpretable) if the \emph{true} MIC could be at either side of the breakpoint.
+\item This is the only mode that preserves uncertainty for ECOFFs.
 }
 
-\code{"standard"} (default)
+\code{"standard"}
 \itemize{
-\item \code{<=} and \code{>=} return \code{"NI"} (non-interpretable) if the MIC is within the breakpoint guideline range.
-\item \code{<} and \code{>} are treated as-is.
+\item \code{<=} and \code{>=} return \code{"NI"} (non-interpretable) if the \emph{true} MIC could be at either side of the breakpoint.
+\item \code{<} always returns \code{"S"}, regardless of the breakpoint.
+\item \code{>} always returns \code{"R"}, regardless of the breakpoint.
 }
 
-\code{"inverse"}
+\code{"lenient"}
 \itemize{
-\item \code{<=} and \code{>=} are treated as-is.
-\item \code{<} always returns \code{"S"}, and \code{>} always returns \code{"R"}.
+\item \code{<=} and \code{<} always return \code{"S"}, regardless of the breakpoint.
+\item \code{>=} and \code{>} always return \code{"R"}, regardless of the breakpoint.
 }
 
-The default \code{"standard"} setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option \code{\link[=AMR-options]{AMR_capped_mic_handling}}.}
+The default \code{"conservative"} setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option \code{\link[=AMR-options]{AMR_capped_mic_handling}}.}
 
-\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).}
+\item{as_wt_nwt}{A \link{logical} to return \code{"WT"}/\code{"NWT"} instead of \code{"S"}/\code{"R"}. Defaults to \code{TRUE} when using ECOFFs, i.e., when \code{breakpoint_type} is set to \code{"ECOFF"}.}
+
+\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).}
 
 \item{reference_data}{A \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
 
@@ -179,7 +186,7 @@ your_data \%>\% mutate_if(is.mic, as.sir, host = "column_with_animal_species", g
 # fast processing with parallel computing:
 as.sir(your_data, ..., parallel = TRUE)
 }\if{html}{\out{</div>}}
-\item Operators like "<=" will be stripped before interpretation. When using \code{capped_mic_handling = "conservative"}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{capped_mic_handling = "standard"}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
+\item Operators like "<=" will be considered according to the \code{capped_mic_handling} setting. At default, an MIC value of e.g. ">2" will return "NI" (non-interpretable) if the breakpoint is 4-8; the \emph{true} MIC could be at either side of the breakpoint. This is to prevent that capped values from raw laboratory data would not be treated conservatively.
 \item \strong{Note:} When using CLSI as the guideline, MIC values must be log2-based doubling dilutions. Values not in this format, will be automatically rounded up to the nearest log2 level as CLSI instructs, and a warning will be thrown.
 }
 \item For \strong{interpreting disk diffusion diameters} according to EUCAST or CLSI. You must clean your disk zones first using \code{\link[=as.disk]{as.disk()}}, that also gives your columns the new data class \code{\link{disk}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
@@ -240,9 +247,9 @@ Regarding choice of veterinary guidelines, these might be the best options to se
 
 \subsection{After Interpretation}{
 
-After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=eucast_rules]{eucast_rules()}} defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
+After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=interpretive_rules]{interpretive_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
 
-To determine which isolates are multi-drug resistant, be sure to run \code{\link[=mdro]{mdro()}} (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about \link[=mdro]{interpreting multidrug-resistant organisms here}.
+To determine which isolates are multi-drug resistant, be sure to run \code{\link[=mdro]{mdro()}} (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about \link[=mdro]{detecting multidrug-resistant organisms here}.
 }
 
 \subsection{Other}{
@@ -258,7 +265,7 @@ The function \code{\link[=is_sir_eligible]{is_sir_eligible()}} returns \code{TRU
 }
 \section{Interpretation of SIR}{
 
-In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}).
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
 
 This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
 }
@@ -442,6 +449,10 @@ as.sir(
 
 as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
 as.sir("<= 0.002; S") # will return "S"
+
+as.sir(c(1, 2, 3))
+as.sir(c(1, 2, 3), S = 3, I = 2, R = 1)
+
 sir_data <- as.sir(c(rep("S", 474), rep("I", 36), rep("R", 370)))
 is.sir(sir_data)
 plot(sir_data) # for percentages

man/av_property.Rd

@@ -74,7 +74,7 @@ The function \code{\link[=av_url]{av_url()}} will return the direct URL to the o
 
 World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 
-European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
+European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
 }
 
 \section{Download Our Reference Data}{

man/bug_drug_combinations.Rd

@@ -45,7 +45,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname,
     decimal point.}
 }
 \value{
-The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} returns a \link{data.frame} with columns "mo", "ab", "S", "SDD", "I", "R", and "total".
+The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} returns a \link{data.frame} with columns "mo", "ab", "S", "SDD", "I", "R", "WT, "NWT", and "total".
 }
 \description{
 Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{\link[=format]{format()}} on the result to prettify it to a publishable/printable format, see \emph{Examples}.

man/clinical_breakpoints.Rd

@@ -27,7 +27,7 @@ A \link[tibble:tibble]{tibble} with 40 217 observations and 14 variables:
 clinical_breakpoints
 }
 \description{
-Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
+Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This data set contains breakpoints for humans, 7 different animal groups, and ECOFFs.
 
 These breakpoints are currently implemented:
 \itemize{

man/count.Rd

@@ -14,9 +14,11 @@
 \alias{count_df}
 \title{Count Available Isolates}
 \usage{
-count_resistant(..., only_all_tested = FALSE)
+count_resistant(..., only_all_tested = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST"))
 
-count_susceptible(..., only_all_tested = FALSE)
+count_susceptible(..., only_all_tested = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST"))
 
 count_S(..., only_all_tested = FALSE)
 
@@ -40,6 +42,14 @@ count_df(data, translate_ab = "name", language = get_AMR_locale(),
 
 \item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see section \emph{Combination Therapy} below.}
 
+\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}. With EUCAST, the 'I' category will be considered as susceptible (see \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}{EUCAST website}), but with with CLSI, it will be considered resistant. Therefore:
+\itemize{
+\item EUCAST: \code{\link[=count_susceptible]{count_susceptible()}} \eqn{= N_{S} + N_{I}}, \code{\link[=count_resistant]{count_resistant()}} \eqn{= N_{R}}
+\item CLSI: \code{\link[=count_susceptible]{count_susceptible()}} \eqn{= N_{S} + N_{SDD}}, \code{\link[=count_resistant]{count_resistant()}} \eqn{= N_{I} + N_{R}}
+}
+
+You can also use e.g. \code{\link[=count_R]{count_R()}} or \code{\link[=count_S]{count_S()}} instead, to be explicit.}
+
 \item{data}{A \link{data.frame} containing columns with class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}}).}
 
 \item{translate_ab}{A column name of the \link{antimicrobials} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}.}
@@ -59,15 +69,13 @@ These functions can be used to count resistant/susceptible microbial isolates. A
 \details{
 These functions are meant to count isolates. Use the \code{\link[=resistance]{resistance()}}/\code{\link[=susceptibility]{susceptibility()}} functions to calculate microbial resistance/susceptibility.
 
-The function \code{\link[=count_resistant]{count_resistant()}} is equal to the function \code{\link[=count_R]{count_R()}}. The function \code{\link[=count_susceptible]{count_susceptible()}} is equal to the function \code{\link[=count_SI]{count_SI()}}.
-
-The function \code{\link[=n_sir]{n_sir()}} is an alias of \code{\link[=count_all]{count_all()}}. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to \code{n_distinct()}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
+The function \code{\link[=n_sir]{n_sir()}} is an alias of \code{\link[=count_all]{count_all()}}. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to \code{dplyr}'s \code{n_distinct()}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
 
 The function \code{\link[=count_df]{count_df()}} takes any variable from \code{data} that has an \code{\link{sir}} class (created with \code{\link[=as.sir]{as.sir()}}) and counts the number of S's, I's and R's. It also supports grouped variables. The function \code{\link[=sir_df]{sir_df()}} works exactly like \code{\link[=count_df]{count_df()}}, but adds the percentage of S, I and R.
 }
 \section{Interpretation of SIR}{
 
-In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}).
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
 
 This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
 }

man/custom_eucast_rules.Rd

@@ -19,7 +19,7 @@ Define custom EUCAST rules for your organisation or specific analysis and use th
 Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the \code{\link[=eucast_rules]{eucast_rules()}} function.
 \subsection{Basics}{
 
-If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
+If you are familiar with the \code{\link[dplyr:case-and-replace-when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
                          TZP == "R" ~ aminopenicillins == "R")
@@ -98,42 +98,45 @@ x
 #>      amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
 }\if{html}{\out{</div>}}
 
-These 35 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
+These 38 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
 \itemize{
 \item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
-\item aminopenicillins\cr(amoxicillin and ampicillin)
+\item aminopenicillins\cr(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)
 \item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)
-\item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
-\item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)
-\item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
-\item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)
-\item cephalosporins\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
+\item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
+\item betalactamase_inhibitors\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, avibactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/sulbactam, ceftaroline/avibactam, ceftazidime/avibactam, ceftolozane/tazobactam, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, nacubactam, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, sulbactam, sultamicillin, taniborbactam, tazobactam, ticarcillin/clavulanic acid, and zidebactam)
+\item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)
+\item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
+\item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, taniborbactam, and tebipenem)
+\item cephalosporins\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
 \item cephalosporins_1st\cr(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)
 \item cephalosporins_2nd\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)
 \item cephalosporins_3rd\cr(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)
-\item cephalosporins_4th\cr(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)
+\item cephalosporins_4th\cr(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)
 \item cephalosporins_5th\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)
-\item cephalosporins_except_caz\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
+\item cephalosporins_except_caz\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
 \item fluoroquinolones\cr(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
 \item glycopeptides\cr(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)
 \item glycopeptides_except_lipo\cr(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)
 \item isoxazolylpenicillins\cr(cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test)
-\item lincosamides\cr(clindamycin, lincomycin, and pirlimycin)
+\item lincosamides\cr(clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin)
 \item lipoglycopeptides\cr(dalbavancin, oritavancin, and telavancin)
-\item macrolides\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)
+\item macrolides\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)
 \item monobactams\cr(aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam)
 \item nitrofurans\cr(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone)
 \item oxazolidinones\cr(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)
 \item penicillins\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid)
 \item phenicols\cr(chloramphenicol, florfenicol, and thiamphenicol)
+\item phosphonics\cr(amikacin/fosfomycin and fosfomycin)
 \item polymyxins\cr(colistin, polymyxin B, and polymyxin B/polysorbate 80)
-\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
+\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
 \item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)
+\item spiropyrimidinetriones\cr(zoliflodacin)
 \item streptogramins\cr(pristinamycin and quinupristin/dalfopristin)
-\item sulfonamides\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea)
-\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline)
-\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test)
-\item trimethoprims\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)
+\item sulfonamides\cr(isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole)
+\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline)
+\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tetracycline/oleandomycin)
+\item trimethoprims\cr(brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)
 \item ureidopenicillins\cr(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)
 }
 }

man/custom_mdro_guideline.Rd

@@ -26,7 +26,7 @@ Define custom a MDRO guideline for your organisation or specific analysis and us
 Using a custom MDRO guideline is of importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
 \subsection{Basics}{
 
-If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
+If you are familiar with the \code{\link[dplyr:case-and-replace-when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
                                 ERY == "R" & age > 60 ~ "Elderly Type B")
@@ -94,39 +94,41 @@ You can define antimicrobial groups instead of single antimicrobials for the rul
 )
 }\if{html}{\out{</div>}}
 
-All 35 antimicrobial selectors are supported for use in the rules:
+All 38 antimicrobial selectors are supported for use in the rules:
 \itemize{
 \item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high
-\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin and ampicillin
+\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, and ampicillin
 \item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole
-\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin
-\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam
-\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid
-\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem
-\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef
+\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin
+\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam
+\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid
+\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, taniborbactam, and tebipenem
+\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef
 \item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine
 \item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef
 \item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef
-\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome
+\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome
 \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam
 \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
 \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod
 \item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test
-\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin, lincomycin, and pirlimycin
+\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin
 \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin, oritavancin, and telavancin
-\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin
+\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin
 \item \code{\link[=monobactams]{monobactams()}} can select: \cr aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam
 \item \code{\link[=nitrofurans]{nitrofurans()}} can select: \cr furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone
 \item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone
 \item \code{\link[=penicillins]{penicillins()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid
 \item \code{\link[=phenicols]{phenicols()}} can select: \cr chloramphenicol, florfenicol, and thiamphenicol
+\item \code{\link[=phosphonics]{phosphonics()}} can select: \cr amikacin/fosfomycin and fosfomycin
 \item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin, polymyxin B, and polymyxin B/polysorbate 80
-\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
+\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
 \item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine
+\item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin
 \item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin and quinupristin/dalfopristin
-\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea
-\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline
-\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole
+\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole
+\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline
+\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole
 \item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam
 }
 }

man/dosage.Rd

@@ -12,7 +12,7 @@ A \link[tibble:tibble]{tibble} with 759 observations and 9 variables:
 \item \code{type}\cr Type of the dosage, either "high_dosage", "standard_dosage", or "uncomplicated_uti"
 \item \code{dose}\cr Dose, such as "2 g" or "25 mg/kg"
 \item \code{dose_times}\cr Number of times a dose must be administered
-\item \code{administration}\cr Route of administration, either "", "im", "iv", or "oral"
+\item \code{administration}\cr Route of administration, either "", "im", "iv", "oral", or NA
 \item \code{notes}\cr Additional dosage notes
 \item \code{original_txt}\cr Original text in the PDF file of EUCAST
 \item \code{eucast_version}\cr Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either 15, 14, 13.1, 12, or 11

man/esbl_isolates.Rd

@@ -9,7 +9,7 @@ A \link[tibble:tibble]{tibble} with 500 observations and 19 variables:
 \itemize{
 \item \code{esbl}\cr Logical indicator if the isolate is ESBL-producing
 \item \code{genus}\cr Genus of the microorganism
-\item \code{AMC:COL}\cr MIC values for 17 antimicrobial agents, transformed to class \code{\link{mic}} (see \code{\link[=as.mic]{as.mic()}})
+\item \code{AMC:COL}\cr MIC values for 17 antimicrobial drugs, transformed to class \code{\link{mic}} (see \code{\link[=as.mic]{as.mic()}})
 }
 }
 \usage{

man/first_isolate.Rd

@@ -108,26 +108,30 @@ All mentioned methods are covered in the \code{\link[=first_isolate]{first_isola
    - Any difference in key antimicrobial results \tab - \code{first_isolate(x, type = "keyantimicrobials")} \cr
 }
 
-}
 
-\subsection{Isolate-based}{
+\strong{Isolate-based}
+
+\emph{Minimum variables required: Microorganism identifier}
 
 This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the \code{\link[=first_isolate]{first_isolate()}} function. For example, the default setting for \code{include_unknown} (\code{FALSE}) will omit selection of rows without a microbial ID.
-}
 
-\subsection{Patient-based}{
+\strong{Patient-based}
 
-To include every genus-species combination per patient once, set the \code{episode_days} to \code{Inf}. This method makes sure that no duplicate isolates are selected from the same patient. This method is preferred to e.g. identify the first MRSA finding of each patient to determine the incidence. Conversely, in a large longitudinal data set, this could mean that isolates are \emph{excluded} that were found years after the initial isolate.
-}
+\emph{Minimum variables required: Microorganism identifier, Patient identifier}
 
-\subsection{Episode-based}{
+This method includes every genus-species combination per patient once. This method makes sure that no duplicate isolates are selected from the same patient. This method is preferred to e.g. identify the first MRSA finding of each patient to determine the incidence. Conversely, in a large longitudinal data set, this could mean that isolates are \emph{excluded} that were found years after the initial isolate.
 
-To include every genus-species combination per patient episode once, set the \code{episode_days} to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data or ICU cases, long episodes are common for analysing regional and national data.
+\strong{Episode-based}
+
+\emph{Minimum variables required: Microorganism identifier, Patient identifier, Date}
+
+To include every genus-species combination per patient episode once, set the \code{episode_days} to a sensible number of days. Depending on the type of analysis, this could be e.g., 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data or ICU cases, long episodes are common for analysing regional and national data.
 
 This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant \emph{Staphylococcus aureus} (MRSA) isolate cannot be differentiated from a wildtype \emph{Staphylococcus aureus} isolate.
-}
 
-\subsection{Phenotype-based}{
+\strong{Phenotype-based}
+
+\emph{Minimum variables required: Microorganism identifier, Patient identifier, Date, Antimicrobial test results}
 
 This is a more reliable method, since it also \emph{weighs} the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
 \enumerate{

man/interpretive_rules.Rd

@@ -1,10 +1,12 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/eucast_rules.R
-\name{eucast_rules}
-\alias{eucast_rules}
+% Please edit documentation in R/interpretive_rules.R
+\name{interpretive_rules}
+\alias{interpretive_rules}
 \alias{EUCAST}
+\alias{eucast_rules}
+\alias{clsi_rules}
 \alias{eucast_dosage}
-\title{Apply EUCAST Rules}
+\title{Apply Interpretive Rules}
 \source{
 \itemize{
 \item EUCAST Expert Rules. Version 2.0, 2012.\cr
@@ -19,13 +21,22 @@ Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility test
 }
 }
 \usage{
-eucast_rules(x, col_mo = NULL, info = interactive(),
-  rules = getOption("AMR_eucastrules", default = c("breakpoints",
-  "expected_phenotypes")), verbose = FALSE, version_breakpoints = 15,
+interpretive_rules(x, col_mo = NULL, info = interactive(),
+  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
+  "expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"),
+  verbose = FALSE, version_breakpoints = 15,
   version_expected_phenotypes = 1.2, version_expertrules = 3.3,
   ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
   custom_rules = NULL, overwrite = FALSE, ...)
 
+eucast_rules(x, col_mo = NULL, info = interactive(),
+  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
+  "expected_phenotypes")), ...)
+
+clsi_rules(x, col_mo = NULL, info = interactive(),
+  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
+  "expected_phenotypes")), ...)
+
 eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
 }
 \arguments{
@@ -35,7 +46,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
 
 \item{info}{A \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.}
 
-\item{rules}{A \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expected_phenotypes"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expected_phenotypes")}. The default value can be set to another value using the package option \code{\link[=AMR-options]{AMR_eucastrules}}: \code{options(AMR_eucastrules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
+\item{rules}{A \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expected_phenotypes"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expected_phenotypes")}. The default value can be set to another value using the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}: \code{options(AMR_interpretive_rules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
+
+\item{guideline}{A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}.}
 
 \item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}
 
@@ -57,15 +70,19 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
 
 \item{ab}{Any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
 
-\item{administration}{Route of administration, either "", "im", "iv", or "oral".}
+\item{administration}{Route of administration, either "", "im", "iv", "oral", or NA.}
 }
 \value{
 The input of \code{x}, possibly with edited values of antimicrobials. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.
 }
 \description{
-Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://www.eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get a \link{data.frame} with advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.
+\strong{WORK IN PROGRESS}
 
-To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see \emph{Details}.
+\strong{The \code{interpretive_rules()} function is new, to allow CLSI 'rules' too. The old \code{eucast_rules()} function will stay as a wrapper, but we need to generalise more parts of the underlying code to allow more than just EUCAST.}
+
+Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://www.eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get a \link{data.frame} with advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.
+
+To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see \emph{Details}.
 }
 \details{
 \strong{Note:} This function does not translate MIC values to SIR values. Use \code{\link[=as.sir]{as.sir()}} for that. \cr
@@ -93,7 +110,7 @@ Before further processing, two non-EUCAST rules about drug combinations can be a
 
 Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
 
-Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the package option \code{\link[=AMR-options]{AMR_eucastrules}}, i.e. run \code{options(AMR_eucastrules = "all")}.
+Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}, i.e. run \code{options(AMR_interpretive_rules = "all")}.
 }
 }
 \section{Download Our Reference Data}{

man/intrinsic_resistant.Rd

@@ -18,7 +18,7 @@ intrinsic_resistant
 Data set containing 'EUCAST Expected Resistant Phenotypes' of \emph{all} bug-drug combinations between the \link{microorganisms} and \link{antimicrobials} data sets.
 }
 \details{
-This data set is currently based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023).
+This data set is currently based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023).
 
 This data set is internally used by:
 \itemize{

man/mdro.Rd

@@ -57,7 +57,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
 
 \item{combine_SI}{A \link{logical} to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the \code{\link[=mdro]{mdro()}} function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using \code{combine_SI = FALSE}, resistance is considered when isolates are R or I.}
 
-\item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
+\item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
 
 \item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}
 
@@ -136,7 +136,7 @@ Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom
 }
 \section{Interpretation of SIR}{
 
-In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}).
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
 
 This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
 }

man/microorganisms.Rd

@@ -13,12 +13,12 @@ A \link[tibble:tibble]{tibble} with 78 679 observations and 26 variables:
 \item \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}\cr Taxonomic rank of the microorganism. Note that for fungi, \emph{phylum} is equal to their taxonomic \emph{division}. Also, for fungi, \emph{subkingdom} and \emph{subdivision} were left out since they do not occur in the bacterial taxonomy.
 \item \code{rank}\cr Text of the taxonomic rank of the microorganism, such as \code{"species"} or \code{"genus"}
 \item \code{ref}\cr Author(s) and year of related scientific publication. This contains only the \emph{first surname} and year of the \emph{latest} authors, e.g. "Wallis \emph{et al.} 2006 \emph{emend.} Smith and Jones 2018" becomes "Smith \emph{et al.}, 2018". This field is directly retrieved from the source specified in the column \code{source}. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.
-\item \code{oxygen_tolerance} \cr Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3\% of all ~39 000 bacteria in the data set contain an oxygen tolerance.
+\item \code{oxygen_tolerance} \cr Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", "microaerophile", or NA. These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3\% of all ~39 000 bacteria in the data set contain an oxygen tolerance.
 \item \code{source}\cr Either "GBIF", "LPSN", "Manually added", "MycoBank", or "manually added" (see \emph{Source})
 \item \code{lpsn}\cr Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, \emph{Acetobacter ascendens} has LPSN Record number 7864 and 11011. Only the first is available in the \code{microorganisms} data set. \emph{\strong{This is a unique identifier}}, though available for only ~33 000 records.
 \item \code{lpsn_parent}\cr LPSN identifier of the parent taxon
 \item \code{lpsn_renamed_to}\cr LPSN identifier of the currently valid taxon
-\item \code{mycobank}\cr Identifier ('MycoBank #') of MycoBank. \emph{\strong{This is a unique identifier}}, though available for only ~18 000 records.
+\item \code{mycobank}\cr Identifier ('MycoBank #') of MycoBank. \emph{\strong{This is a unique identifier}}, though available for only ~19 000 records.
 \item \code{mycobank_parent}\cr MycoBank identifier of the parent taxon
 \item \code{mycobank_renamed_to}\cr MycoBank identifier of the currently valid taxon
 \item \code{gbif}\cr Identifier ('taxonID') of Global Biodiversity Information Facility (GBIF). \emph{\strong{This is a unique identifier}}, though available for only ~49 000 records.
@@ -70,7 +70,7 @@ Included taxonomic data from \href{https://lpsn.dsmz.de}{LPSN}, \href{https://ww
 \item ~28 000 species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histoplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
 \item ~8 100 (sub)species from the kingdom of Protozoa
 \item ~1 600 (sub)species from 39 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
-\item All ~22 000 previously accepted names of all included (sub)species (these were taxonomically renamed)
+\item All ~26 000 previously accepted names of all included (sub)species (these were taxonomically renamed)
 \item The complete taxonomic tree of all included (sub)species: from kingdom to subspecies
 \item The identifier of the parent taxons
 \item The year and first author of the related scientific publication

man/mo_property.Rd

@@ -197,7 +197,7 @@ Determination of the Gram stain (\code{\link[=mo_gramstain]{mo_gramstain()}}) wi
 
 Determination of yeasts (\code{\link[=mo_is_yeast]{mo_is_yeast()}}) will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. \emph{True yeasts} quite specifically refers to yeasts in the underlying order Saccharomycetales (such as \emph{Saccharomyces cerevisiae}). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}).
 
-Determination of intrinsic resistance (\code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}) will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antimicrobials).
+Determination of intrinsic resistance (\code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}) will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antimicrobials).
 
 Determination of bacterial oxygen tolerance (\code{\link[=mo_oxygen_tolerance]{mo_oxygen_tolerance()}}) will be based on BacDive, see \emph{Source}. The function \code{\link[=mo_is_anaerobic]{mo_is_anaerobic()}} only returns \code{TRUE} if the oxygen tolerance is \code{"anaerobe"}, indicting an obligate anaerobic species or genus. It always returns \code{FALSE} for species outside the taxonomic kingdom of Bacteria.
 

man/plot.Rd

@@ -172,12 +172,20 @@ Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC
 \details{
 \subsection{The \verb{scale_*_mic()} Functions}{
 
-The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the operators in MIC values (such as \code{>=}) if desired. Missing intermediate log2 levels will be plotted too.
+The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale.
+
+There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class \link[=as.mic]{mic}.
+
+When manually added though, they allow to rescale the MIC range with an 'inside' or 'outside' range if required, and provide the option to retain the operators in MIC values (such as \code{>=}). Missing intermediate log2 levels will always be plotted too.
 }
 
 \subsection{The \verb{scale_*_sir()} Functions}{
 
-The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} functions allow to plot the \link[=as.sir]{sir} class in the right order (S < SDD < I < R < NI). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 28 supported languages (use \code{language = NULL} to keep S/I/R). Also, except for \code{\link[=scale_x_sir]{scale_x_sir()}}, they set colour-blind friendly colours to the \code{colour} and \code{fill} aesthetics.
+The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} functions allow to plot the \link[=as.sir]{sir} class in the right order (S < SDD < I < R < NI < WT < NWT < NS).
+
+There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class \link[=as.sir]{sir}.
+
+At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 28 supported languages (use \code{language = NULL} to keep S/I/R). Also, except for \code{\link[=scale_x_sir]{scale_x_sir()}}, they set colour-blind friendly colours to the \code{colour} and \code{fill} aesthetics.
 }
 
 \subsection{Additional \code{ggplot2} Functions}{
@@ -235,17 +243,12 @@ if (require("ggplot2")) {
   ) +
     geom_col()
   mic_plot +
-    labs(title = "without scale_x_mic()")
+    labs(title = "scale_x_mic() automatically applied")
 }
 if (require("ggplot2")) {
   mic_plot +
-    scale_x_mic() +
-    labs(title = "with scale_x_mic()")
-}
-if (require("ggplot2")) {
-  mic_plot +
-    scale_x_mic(keep_operators = "all") +
-    labs(title = "with scale_x_mic() keeping all operators")
+    scale_x_mic(keep_operators = "none") +
+    labs(title = "with scale_x_mic() keeping no operators")
 }
 if (require("ggplot2")) {
   mic_plot +
@@ -272,7 +275,7 @@ if (require("ggplot2")) {
   ) +
     geom_boxplot() +
     geom_violin(linetype = 2, colour = "grey30", fill = NA) +
-    scale_y_mic()
+    labs(title = "scale_y_mic() automatically applied")
 }
 if (require("ggplot2")) {
   ggplot(
@@ -304,7 +307,7 @@ if (require("ggplot2")) {
 
 # Plotting using scale_y_mic() and scale_colour_sir() ------------------
 if (require("ggplot2")) {
-  plain <- ggplot(
+  mic_sir_plot <- ggplot(
     data.frame(
       mic = some_mic_values,
       group = some_groups,
@@ -318,21 +321,16 @@ if (require("ggplot2")) {
     theme_minimal() +
     geom_boxplot(fill = NA, colour = "grey30") +
     geom_jitter(width = 0.25)
+    labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
 
-  plain
+  mic_sir_plot
 }
 if (require("ggplot2")) {
-  # and now with our MIC and SIR scale functions:
-  plain +
-    scale_y_mic() +
-    scale_colour_sir()
-}
-if (require("ggplot2")) {
-  plain +
+  mic_sir_plot +
     scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
     scale_colour_sir(
-      language = "pt",
-      name = "Support in 27 languages"
+      language = "pt", # Portuguese
+      name = "Support in 28 languages"
     )
 }
 }

man/proportion.Rd

@@ -19,10 +19,12 @@
 }
 \usage{
 resistance(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+  only_all_tested = FALSE, guideline = getOption("AMR_guideline",
+  "EUCAST"))
 
 susceptibility(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+  only_all_tested = FALSE, guideline = getOption("AMR_guideline",
+  "EUCAST"))
 
 sir_confidence_interval(..., ab_result = "R", minimum = 30,
   as_percent = FALSE, only_all_tested = FALSE, confidence_level = 0.95,
@@ -60,6 +62,14 @@ sir_df(data, translate_ab = "name", language = get_AMR_locale(),
 
 \item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see section \emph{Combination Therapy} below.}
 
+\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}. With EUCAST, the 'I' category will be considered as susceptible (see \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}{EUCAST website}), but with with CLSI, it will be considered resistant. Therefore:
+\itemize{
+\item EUCAST: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%I}, \code{\link[=resistance]{resistance()}} \eqn{= \%R}
+\item CLSI: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%SDD}, \code{\link[=resistance]{resistance()}} \eqn{= \%I + \%R}
+}
+
+You can also use e.g. \code{\link[=proportion_R]{proportion_R()}} or \code{\link[=proportion_S]{proportion_S()}} instead, to be explicit.}
+
 \item{ab_result}{Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".}
 
 \item{confidence_level}{The confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using \code{\link[=binom.test]{binom.test()}}, i.e., the Clopper-Pearson method.}
@@ -136,7 +146,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
 
 \section{Interpretation of SIR}{
 
-In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}).
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
 
 This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
 }