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(v2.1.1.9198) support eucast expert rules 14 and 13.1

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dr. M.S. (Matthijs) Berends 2025-03-14 10:10:35 +01:00
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DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 2.1.1.9197
Date: 2025-03-13
Version: 2.1.1.9198
Date: 2025-03-14
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

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NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9197
# AMR 2.1.1.9198
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
@ -61,8 +61,8 @@ This package now supports not only tools for AMR data analysis in clinical setti
* The selectors `lincosamides()` and `macrolides()` do not overlap anymore - each antibiotic is now classified as either of these and not both
* Fixed selector `fluoroquinolones()`, which now really only selects second-generation quinolones and up (first-generation quinolones do not contain a fluorine group)
* `antimicrobials` data set
* Added agents used for screening, with an ID all ending with `-S`: benzylpenicillin screening test (`PEN-S`), beta-lactamase screening test (`BTL-S`), clindamycin inducible screening test (`CLI-S`), nalidixic acid screening test (`NAL-S`), norfloxacin screening test (`NOR-S`), oxacillin screening test (`OXA-S`), pefloxacin screening test (`PEF-S`), and tetracycline screening test (`TCY-S`). The ID of cefoxitin screening was renamed from `FOX1` to `FOX-S`, while the old code remains to work.
* For this reason, the antimicrobial selectors `lincosamides()`, `isoxazolylpenicillins()`, `quinolones()`, `fluoroquinolones()`, `tetracyclines()` now contain the argument `only_treatable = TRUE` (similar to other antimicrobial selectors that contain non-treatable drugs)
* Added agents used for screening, with an ID all ending with `-S`: benzylpenicillin screening test (`PEN-S`), beta-lactamase screening test (`BTL-S`), cefotaxime screening test (`CTX-S`), clindamycin inducible screening test (`CLI-S`), nalidixic acid screening test (`NAL-S`), norfloxacin screening test (`NOR-S`), oxacillin screening test (`OXA-S`), pefloxacin screening test (`PEF-S`), and tetracycline screening test (`TCY-S`). The ID of cefoxitin screening was renamed from `FOX1` to `FOX-S`, while the old code remains to work.
* For this reason, the antimicrobial selectors `cephalosporins()`, `cephalosporins_3rd()`, `lincosamides()`, `isoxazolylpenicillins()`, `quinolones()`, `fluoroquinolones()`, and `tetracyclines()` now contain the argument `only_treatable = TRUE` (similar to other antimicrobial selectors that contain non-treatable drugs)
* Added amorolfine (`AMO`, D01AE16), which is now also part of the `antifungals()` selector
* Added efflux (`EFF`), to allow mapping to AMRFinderPlus
* Added tigemonam (`TNM`), a monobactam
@ -75,7 +75,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Comparisons of MIC values are now more strict. For example, `>32` is higher than (and never equal to) `32`. Thus, `as.mic(">32") == as.mic(32)` now returns `FALSE`, and `as.mic(">32") > as.mic(32)` now returns `TRUE`.
* Sorting of MIC values (using `sort()`) was fixed in the same manner; `<0.001` now gets sorted before `0.001`, and `>0.001` gets sorted after `0.001`.
* Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range
* `eucast_rules()` now has an argument `overwrite` (default: `TRUE`) to indicate whether non-`NA` values should be overwritten
* `eucast_rules()` now has an argument `overwrite` (default: `FALSE`) to indicate whether non-`NA` values should be overwritten
* Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (`as.disk()`) is now between 0 and 50 mm
* Updated `italicise_taxonomy()` to support HTML output
* `custom_eucast_rules()` now supports multiple antibiotics and antibiotic groups to be affected by a single rule

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PythonPackage/AMR/AMR.egg-info/PKG-INFO
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Metadata-Version: 2.2
Name: AMR
Version: 2.1.1.9197
Version: 2.1.1.9198
Summary: A Python wrapper for the AMR R package
Home-page: https://github.com/msberends/AMR
Author: Matthijs Berends

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PythonPackage/AMR/dist/amr-2.1.1.9197.tar.gz vendored
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PythonPackage/AMR/dist/amr-2.1.1.9197-py3-none-any.whl → PythonPackage/AMR/dist/amr-2.1.1.9198-py3-none-any.whl vendored
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PythonPackage/AMR/setup.py
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@ -2,7 +2,7 @@ from setuptools import setup, find_packages
setup(
name='AMR',
version='2.1.1.9197',
version='2.1.1.9198',
packages=find_packages(),
install_requires=[
'rpy2',

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R/aa_globals.R
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@ -30,12 +30,18 @@
# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
# (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file)
EUCAST_VERSION_BREAKPOINTS <- list(
# "13.0" = list(
# version_txt = "v13.0",
# year = 2023,
# title = "'EUCAST Clinical Breakpoint Tables'",
# url = "https://www.eucast.org/clinical_breakpoints/"
# ),
"14.0" = list(
version_txt = "v14.0",
year = 2024,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/"
),
"13.1" = list(
version_txt = "v13.1",
year = 2023,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/"
),
"12.0" = list(
version_txt = "v12.0",
year = 2022,

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R/ab.R
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@ -211,6 +211,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
next
}
# screening, but written without the hyphen, e.g., FOXS instead of FOX-S
if (substr(x[i], 4, 4) == "S" && paste0(substr(x[i], 1, 3), "-S") %in% AMR_env$AB_lookup$ab) {
x_new[i] <- paste0(substr(x[i], 1, 3), "-S")
next
}
if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], translate_ab = FALSE)[[1]]),
error = function(e) character(0)
@ -306,7 +312,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
next
}
# try if name ends with it
found <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
if (nchar(x[i]) >= 4 && length(found) > 0) {

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R/amr_selectors.R
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@ -290,10 +290,10 @@ carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_
#' @rdname antimicrobial_selectors
#' @export
cephalosporins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
cephalosporins <- function(only_sir_columns = FALSE, only_treatable = TRUE, 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("cephalosporins", only_sir_columns = only_sir_columns, return_all = return_all)
amr_select_exec("cephalosporins", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
}
#' @rdname antimicrobial_selectors
@ -314,10 +314,10 @@ cephalosporins_2nd <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
#' @rdname antimicrobial_selectors
#' @export
cephalosporins_3rd <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
cephalosporins_3rd <- function(only_sir_columns = FALSE, only_treatable = TRUE, 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("cephalosporins_3rd", only_sir_columns = only_sir_columns, return_all = return_all)
amr_select_exec("cephalosporins_3rd", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
}
#' @rdname antimicrobial_selectors

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R/data.R
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@ -306,6 +306,8 @@
#' ### Imported from WHONET
#' Clinical breakpoints in this package were validated through and imported from [WHONET](https://whonet.org), a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on [their website](https://whonet.org). The developers of WHONET and this `AMR` package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.
#'
#' Our import and reproduction script can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_clinical_breakpoints.R>.
#'
#' ### Response from CLSI and EUCAST
#' The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this `AMR` package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, WHO, developers of WHONET software, and developers of this `AMR` package.
#'

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R/eucast_rules.R
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@ -72,7 +72,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @param administration route of administration, either `r vector_or(dosage$administration)`
#' @param only_sir_columns a [logical] to indicate whether only antimicrobial columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`)
#' @param custom_rules custom rules to apply, created with [custom_eucast_rules()]
#' @param overwrite a [logical] to indicate whether non-`NA` values must be overwritten (defaults to `TRUE`). With `FALSE`, only `NA` values are changed.
#' @param overwrite A [logical] indicating whether to overwrite non-`NA` values (default: `FALSE`). When `FALSE`, only `NA` values are modified. To ensure compliance with EUCAST guidelines, **this should remain** `FALSE`, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant."
#' @inheritParams first_isolate
#' @details
#' **Note:** This function does not translate MIC values to SIR values. Use [as.sir()] for that. \cr
@ -167,13 +167,13 @@ eucast_rules <- function(x,
info = interactive(),
rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
verbose = FALSE,
version_breakpoints = 12.0,
version_breakpoints = 14.0,
version_expertrules = 3.3,
# TODO version_resistant_phenotypes = 1.2,
ampc_cephalosporin_resistance = NA,
only_sir_columns = FALSE,
custom_rules = NULL,
overwrite = TRUE,
overwrite = FALSE,
...) {
meet_criteria(x, allow_class = "data.frame")
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
@ -630,10 +630,10 @@ eucast_rules <- function(x,
# sometimes, the screenings are missing but the names are actually available
# we only hints on remaining rows in `eucast_rules_df`
screening_abx <- c("FOX", "BTL", "CLI", "NAL", "NOR", "OXA", "PEF", "PEN", "TCY")
screening_abx <- as.character(AMR::antimicrobials$ab[which(AMR::antimicrobials$ab %like% "-S$")])
screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(EUCAST_RULES_DF$and_these_antibiotics[!is.na(EUCAST_RULES_DF$and_these_antibiotics)], ", *")))]
for (ab in screening_abx) {
ab_s <- paste0(ab, "-S")
for (ab_s in screening_abx) {
ab <- gsub("-S$", "", ab_s)
if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
if (isTRUE(info)) {
message_("Using column '", cols_ab[names(cols_ab) == ab],
@ -1130,7 +1130,7 @@ edit_sir <- function(x,
if (any(!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir), na.rm = TRUE)) {
track_changes$sir_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir)]
}
non_SIR <- !(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")
non_SIR <- is.na(new_edits[rows, cols]) | !(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")
tryCatch(
# insert into original table
if (isTRUE(overwrite)) {

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data-raw/_pre_commit_checks.R
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@ -636,8 +636,12 @@ styler::style_pkg(include_roxygen_examples = FALSE,
exclude_dirs = list.dirs(full.names = FALSE, recursive = FALSE)[!list.dirs(full.names = FALSE, recursive = FALSE) %in% c("R", "tests")])
# Document pkg ------------------------------------------------------------
usethis::ui_info("Documenting package")
suppressMessages(devtools::document(quiet = TRUE))
if (interactive()) {
message("Skipping document in interactive mode")
} else {
usethis::ui_info("Documenting package")
suppressMessages(devtools::document(quiet = TRUE))
}
# Finished ----------------------------------------------------------------
usethis::ui_done("All done")

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data-raw/ab.md5
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b52ea0014f63a73b9369475611c74644
69d8a565bed4a1cd564f313e5142ab48

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data-raw/antimicrobials.txt
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@ -92,6 +92,7 @@
"CND" 43507 "Ceforanide" "Cephalosporins (2nd gen.)" "J01DC11" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "ceforanido,ceforanidum,precef,radacef" 4 "g" "103-2,104-0,105-7,106-5,18885-4,55643-1"
"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "NA" "" "cefoselissulfate,wincef,winsef" ""
"CTX" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "J01DD01" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cfot,cft,cftx,ct,ctx,fot,tax,xct" "cefotaxim,cefotaxima,cefotaximaacid,cefotaximeacid,cefotaximhikma,cefotaximum,cephotaxime,claforan,omnatax" 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" "" ""
"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.)" "J01DD51" "cxcl,xctl" "" ""
"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" "NA" "" "" "54191-2,54192-0,54193-8,55644-9"
"CTT" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "J01DC05" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cftt,cn,cte,ctn,ctt,tans" "apacef,cefotan,cefotetanacid,cefotetanfreeacid,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"

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data-raw/eucast_rules.tsv
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@ -235,152 +235,554 @@ genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Br
genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 12
genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 12
genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 12 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 12
genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 12
genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 12
genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 12
genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 12
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species is Staphylococcus aureus "PEN, FOX-S" "S, S" penicillins S Staphylococcus Breakpoints 12
genus_species is Staphylococcus aureus "PEN, FOX-S" "R, S" "betalactams_with_inhibitor, isoxazolylpenicillins, NAF" S Staphylococcus Breakpoints 12
genus is Staphylococcus FOX-S R "PEN, PHN, AMP, AMX, PIP, TIC" R Staphylococcus Breakpoints 12
genus_species is Staphylococcus saprophyticus AMP S "AMP, SAM, AMX, AMC, PIP, TZP" S Staphylococcus Breakpoints 12
genus is Staphylococcus FOX-S S "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" S Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
genus is Staphylococcus FOX-S I "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" I Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
genus is Staphylococcus FOX-S R "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" R Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S R "PEN, PHN, AMP, AMX, PIP, TIC" R Staphylococcus Breakpoints 12
genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S S "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" S Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S I "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" I Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S R "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" R Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 12
genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 12
genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 12
genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 12
genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 12
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 12 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 12 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 12 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S S carbapenems S Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method"
genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S I carbapenems I Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method"
genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S R carbapenems R Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method"
genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 12
genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 12
genus_species is Staphylococcus aureus VAN S DAL, ORI S Staphylococcus Breakpoints 12
genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S Staphylococcus Breakpoints 12 MRSA isolates are in this file safely denoted as FOX resistant
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 12
genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 12
genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Enterococcus Breakpoints 12
genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I Enterococcus Breakpoints 12
genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R Enterococcus Breakpoints 12
genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 12
genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 12
genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 12
genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S Streptococcus groups A, B, C, G Breakpoints 12 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I Streptococcus groups A, B, C, G Breakpoints 12 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R Streptococcus groups A, B, C, G Breakpoints 12 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 12
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 12
genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 12 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 12 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
genus is Staphylococcus NOR-S S "CIP, LVX" I Staphylococcus Breakpoints 12
genus_species is Staphylococcus aureus VAN S "DAL, ORI" S Staphylococcus Breakpoints 12
genus_species is Staphylococcus aureus "FOX-S, VAN" "R, S" TLV S Staphylococcus Breakpoints 12 MRSA isolates are in this file safely denoted as FOX resistant
genus is Staphylococcus ERY S "AZM, CLR, RXT" S Staphylococcus Breakpoints 12
genus is Staphylococcus TCY-S S "DOX, MNO" S Staphylococcus Breakpoints 12
genus is Enterococcus AMP S "AMP, SAM, AMX, AMC, PIP, TZP" S Enterococcus Breakpoints 12
genus is Enterococcus AMP I "AMP, SAM, AMX, AMC, PIP, TZP" I Enterococcus Breakpoints 12
genus is Enterococcus AMP R "AMP, SAM, AMX, AMC, PIP, TZP" R Enterococcus Breakpoints 12
genus is Enterococcus NOR-S S "CIP, LVX" S Enterococcus Breakpoints 12
genus is Enterococcus NOR-S I "CIP, LVX" I Enterococcus Breakpoints 12
genus is Enterococcus NOR-S R "CIP, LVX" R Enterococcus Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN S penicillins S "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN I penicillins I "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN R penicillins R "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species is Streptococcus Group B PEN S "AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP" S "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]"
genus_species is Streptococcus Group B PEN I "AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP" I "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]"
genus_species is Streptococcus Group B PEN R "AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP" R "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]"
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN S cephalosporins S "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN I cephalosporins I "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN R cephalosporins R "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN S carbapenems S "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN I carbapenems I "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN R carbapenems R "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S S MFX S "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S S LVX I "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S R "MFX, LVX" R "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" VAN S "DAL, ORI" S "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" ERY S "AZM, CLR, RXT" S "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" ERY R "AZM, CLR, RXT" R "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" TCY-S S "DOX, MNO" S "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" TCY-S R "DOX, MNO" R "Streptococcus groups A, B, C, G" Breakpoints 12
genus_species is Streptococcus pneumoniae OXA-S S "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP" S Streptococcus pneumoniae Breakpoints 12 "x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2022"" & clinical_breakpoints$mo == as.mo(""S. pneumoniae"") & clinical_breakpoints$ab != as.ab(""cefaclor""))]); sort(c(x[x %in% betalactams()], ""SAM"", ""PIP"", ""TZP"", ""PHN"", ""IMR"", ""MEV""))"
genus_species is Streptococcus pneumoniae PEN S "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP" S Streptococcus pneumoniae Breakpoints 12 "x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2022"" & clinical_breakpoints$mo == as.mo(""S. pneumoniae"") & clinical_breakpoints$ab != as.ab(""cefaclor""))]); sort(c(x[x %in% betalactams()], ""SAM"", ""PIP"", ""TZP"", ""PHN"", ""IMR"", ""MEV""))"
genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 12 from flowchart: when OXA < 20 or PEN > 0.06
genus_species is Streptococcus pneumoniae OXA-S R "PEN, PHN" R Streptococcus pneumoniae Breakpoints 12 from flowchart: when OXA < 20 or PEN > 0.06
genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 12 from flowchart: when OXA < 20 or PEN > 0.06
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae AMP S "AMX, AMC, SAM, PIP, TZP" S Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae AMP I "AMX, AMC, SAM, PIP, TZP" I Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae AMP R "AMX, AMC, SAM, PIP, TZP" R Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 12
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S Haemophilus influenzae Breakpoints 12 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
genus_species is Haemophilus influenzae PEN-S, BTL-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 12
genus_species is Streptococcus pneumoniae NOR-S R "MFX, LVX" R Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae ERY S "AZM, CLR, RXT" S Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae ERY R "AZM, CLR, RXT" R Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae TCY-S S "DOX, MNO" S Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae TCY-S R "DOX, MNO" R Streptococcus pneumoniae Breakpoints 12
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" PEN-S S "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP" S Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" PEN-S R "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP" R Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" AMP S "AMX, AMC, SAM, PIP, TZP" S Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" AMP I "AMX, AMC, SAM, PIP, TZP" I Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" AMP R "AMX, AMC, SAM, PIP, TZP" R Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
genus_species is Haemophilus influenzae PEN-S S "AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP" S Haemophilus influenzae Breakpoints 12 "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2022"" & clinical_breakpoints$mo == as.mo(""H. influenzae""))]), ""IMR"", ""MEV""); sort(x[x %in% betalactams()])"
genus_species is Haemophilus influenzae "PEN-S, BTL-S" "R, R" "AMP, AMX, PIP" R Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 12
genus_species is Moraxella catarrhalis BTL-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R Moraxella catarrhalis Breakpoints 12 penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
genus_species is Haemophilus influenzae NAL-S S "CIP, LVX, MFX, OFX" S Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae NAL-S I "CIP, LVX, MFX, OFX" I Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae NAL-S R "CIP, LVX, MFX, OFX" R Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae TCY S "DOX, MNO" S Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae TCY R "DOX, MNO" R Haemophilus influenzae Breakpoints 12
genus_species is Moraxella catarrhalis BTL-S R "AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC" R Moraxella catarrhalis Breakpoints 12 penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 12
genus_species is Neisseria gonorrhoeae BTL-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 12
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 12
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 12
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 12
genus_species is Moraxella catarrhalis NAL-S S "CIP, LVX, MFX, OFX" S Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis NAL-S R "CIP, LVX, MFX, OFX" R Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis ERY S "AZM, CLR, RXT" S Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis ERY R "AZM, CLR, RXT" R Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis TCY S "DOX, MNO" S Moraxella catarrhalis Breakpoints 12
genus_species is Moraxella catarrhalis TCY R "DOX, MNO" R Moraxella catarrhalis Breakpoints 12
genus_species is Neisseria gonorrhoeae BTL-S R "AMP, AMX" R Neisseria gonorrhoeae Breakpoints 12
genus_species is Neisseria gonorrhoeae "BTL-S, PEN" "S, S" "AMP, AMX" S Neisseria gonorrhoeae Breakpoints 12
genus_species is Neisseria gonorrhoeae "BTL-S, PEN" "S, I" "AMP, AMX" I Neisseria gonorrhoeae Breakpoints 12
genus_species is Neisseria gonorrhoeae "BTL-S, PEN" "S, R" "AMP, AMX" R Neisseria gonorrhoeae Breakpoints 12
genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 12
genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 12
genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 12
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 12
genus is Prevotella PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & mo_genus(clinical_breakpoints$mo) == ""Prevotella"")]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM""); sort(x[x %in% betalactams()])"
genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints
genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints
genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints
genus_species is Fusobacterium necrophorum PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & clinical_breakpoints$mo == as.mo(""Fusobacterium necrophorum""))]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM""); sort(x[x %in% betalactams()])"
genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints
genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints
genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints
genus_species is Clostridium perfringens PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & clinical_breakpoints$mo == as.mo(""Fusobacterium necrophorum""))]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM""); sort(x[x %in% betalactams()])"
genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints
genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints
genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints
genus_species is Cutibacterium acnes PEN S "AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & clinical_breakpoints$mo == as.mo(""Cutibacterium acnes""))]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM"", ""TZP"", ""CTX"", ""CRO""); sort(x[x %in% betalactams()])"
genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints
genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints
genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints
genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints
genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints
genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints
genus_species is Pasteurella multocida PEN S "AMP, AMX" S Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida PEN I "AMP, AMX" I Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida PEN R "AMP, AMX" R Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida NAL-S S "CIP, LVX" S Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida NAL-S R "CIP, LVX" R Pasteurella multocida Breakpoints 12
genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 12
genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 12
genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 12
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 12
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 12
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 12
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 12
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 12
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Kingella kingae BTL-S R PEN, AMP, AMX R Kingella kingae Breakpoints 12
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 12
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 12
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 12
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 12
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 12
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 12
genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY S "AZM, CLR" S Campylobacter coli/jejuni Breakpoints 12
genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY I "AZM, CLR" I Campylobacter coli/jejuni Breakpoints 12
genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY R "AZM, CLR" R Campylobacter coli/jejuni Breakpoints 12
genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY S DOX S Campylobacter coli/jejuni Breakpoints 12
genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY I DOX I Campylobacter coli/jejuni Breakpoints 12
genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY R DOX R Campylobacter coli/jejuni Breakpoints 12
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN S CTX S Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY I DOX I Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 12
genus_species is Kingella kingae BTL-S R "PEN, AMP, AMX" R Kingella kingae Breakpoints 12
genus_species is Kingella kingae PEN S "AMP, AMX" S Kingella kingae Breakpoints 12
genus_species is Kingella kingae PEN I "AMP, AMX" I Kingella kingae Breakpoints 12
genus_species is Kingella kingae PEN R "AMP, AMX" R Kingella kingae Breakpoints 12
genus_species is Kingella kingae ERY S "AZM, CLR" S Kingella kingae Breakpoints 12
genus_species is Kingella kingae ERY I "AZM, CLR" I Kingella kingae Breakpoints 12
genus_species is Kingella kingae ERY R "AZM, CLR" R Kingella kingae Breakpoints 12
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 12
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 12
genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 12
genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 12
genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 12
genus is Vibrio PEF-S S "CIP, LVX" S Vibrio spp. Breakpoints 12
genus is Vibrio PEF-S I "CIP, LVX" I Vibrio spp. Breakpoints 12
genus is Vibrio PEF-S R "CIP, LVX" R Vibrio spp. Breakpoints 12
genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 12
genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 12
genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 12
genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 12
genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 12
genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 12
genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 12
genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 12
genus is Bacillus NOR-S S "CIP, LVX" I Bacillus Breakpoints 12
genus is Bacillus NOR-S R "CIP, LVX" R Bacillus Breakpoints 12
genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 12
genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 12
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 13.1
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 13.1
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 13.1
order is Enterobacterales LEX S CZO I Enterobacterales (Order) Breakpoints 13.1
order is Enterobacterales CFR S CZO I Enterobacterales (Order) Breakpoints 13.1
genus is Salmonella PEF-S S CIP S Enterobacterales (Order) Breakpoints 13.1
genus is Salmonella PEF-S I CIP I Enterobacterales (Order) Breakpoints 13.1
genus is Salmonella PEF-S R CIP R Enterobacterales (Order) Breakpoints 13.1
genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Breakpoints 13.1
genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 13.1
genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 13.1
genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 13.1 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 13.1
genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 13.1
genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 13.1
genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 13.1
genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 13.1
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 13.1
genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 13.1
genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 13.1
genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 13.1
genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 13.1
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 13.1
genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 13.1
genus_species is Staphylococcus aureus VAN S DAL, ORI S Staphylococcus Breakpoints 13.1
genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S Staphylococcus Breakpoints 13.1 MRSA isolates are in this file safely denoted as FOX resistant
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 13.1
genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 13.1
genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Enterococcus Breakpoints 13.1
genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I Enterococcus Breakpoints 13.1
genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R Enterococcus Breakpoints 13.1
genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 13.1
genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 13.1
genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 13.1
genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 13.1 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 13.1 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 13.1
genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 13.1
genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 13.1 from flowchart: when OXA < 20 or PEN > 0.06
genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 13.1 from flowchart: when OXA < 20 or PEN > 0.06
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 13.1
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 13.1
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 13.1
genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 13.1
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 13.1
genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 13.1
genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 13.1
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S Haemophilus influenzae Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
genus_species is Haemophilus influenzae PEN-S, BTL-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 13.1
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 13.1
genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 13.1
genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 13.1
genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 13.1
genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I Haemophilus influenzae Breakpoints 13.1
genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 13.1
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 13.1
genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 13.1
genus_species is Moraxella catarrhalis BTL-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R Moraxella catarrhalis Breakpoints 13.1 penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 13.1
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 13.1
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 13.1
genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 13.1
genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 13.1
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 13.1
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 13.1
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 13.1
genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 13.1
genus_species is Neisseria gonorrhoeae BTL-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 13.1
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 13.1
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 13.1
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 13.1
genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 13.1
genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 13.1
genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 13.1
genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints 13.1
genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints 13.1
genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints 13.1
genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints 13.1
genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints 13.1
genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints 13.1
genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints 13.1
genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints 13.1
genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints 13.1
genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints 13.1
genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints 13.1
genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints 13.1
genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints 13.1
genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints 13.1
genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints 13.1
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 13.1
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 13.1
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 13.1
genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 13.1
genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 13.1
genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 13.1
genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 13.1
genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 13.1
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 13.1
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 13.1
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 13.1
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 13.1
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 13.1
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN S CTX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY I DOX I Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 13.1
genus_species is Kingella kingae BTL-S R PEN, AMP, AMX R Kingella kingae Breakpoints 13.1
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 13.1
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 13.1
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 13.1
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 13.1
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 13.1
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 13.1
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 13.1
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 13.1
genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 13.1
genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 13.1
genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 13.1
genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 13.1
genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 13.1
genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 13.1
genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 13.1
genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 13.1
genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 13.1
genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 13.1
genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 13.1
genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 13.1
genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 13.1
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 14
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 14
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 14
order is Enterobacterales LEX S CZO I Enterobacterales (Order) Breakpoints 14
order is Enterobacterales CFR S CZO I Enterobacterales (Order) Breakpoints 14
genus is Salmonella PEF-S S CIP S Enterobacterales (Order) Breakpoints 14
genus is Salmonella PEF-S I CIP I Enterobacterales (Order) Breakpoints 14
genus is Salmonella PEF-S R CIP R Enterobacterales (Order) Breakpoints 14
genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Breakpoints 14
genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 14
genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 14
genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 14 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 14
genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 14
genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 14
genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 14
genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 14
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 14
genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 14
genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 14
genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 14
genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 14
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 14
genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 14
genus_species is Staphylococcus coagulase-negative VAN, TEC S, S DAL S Staphylococcus Breakpoints 14
genus_species is Staphylococcus aureus VAN S DAL, ORI S Staphylococcus Breakpoints 14
genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S Staphylococcus Breakpoints 14 MRSA isolates are in this file safely denoted as FOX resistant
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 14
genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 14
genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Enterococcus Breakpoints 14
genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I Enterococcus Breakpoints 14
genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R Enterococcus Breakpoints 14
genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 14
genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 14
genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 14
genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 14
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 14
genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 14 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 14 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 14
genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 14
genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 14 from flowchart: when OXA < 20 or PEN > 0.06
genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 14 from flowchart: when OXA < 20 or PEN > 0.06
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 14
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 14
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 14
genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 14
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 14
genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 14
genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 14
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S Haemophilus influenzae Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
genus_species is Haemophilus influenzae PEN-S, BTL-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 14
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 14
genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 14
genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 14
genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 14
genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I Haemophilus influenzae Breakpoints 14
genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 14
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 14
genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 14
genus_species is Moraxella catarrhalis BTL-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R Moraxella catarrhalis Breakpoints 14 penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 14
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 14
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 14
genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 14
genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 14
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 14
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 14
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 14
genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 14
genus_species is Neisseria gonorrhoeae BTL-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 14
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 14
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 14
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 14
genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 14
genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 14
genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 14
genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints 14
genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints 14
genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints 14
genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints 14
genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints 14
genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints 14
genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints 14
genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints 14
genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints 14
genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints 14
genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints 14
genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints 14
genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints 14
genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints 14
genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints 14
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 14
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 14
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 14
genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 14
genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 14
genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 14
genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 14
genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 14
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 14
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 14
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 14
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 14
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 14
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 14
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints 14
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints 14
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints 14
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints 14
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints 14
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints 14
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints 14
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 14
genus_species is Kingella kingae BTL-S R PEN, AMP, AMX R Kingella kingae Breakpoints 14
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 14
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 14
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 14
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 14
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 14
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 14
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 14
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 14
genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 14
genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 14
genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 14
genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 14
genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 14
genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 14
genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 14
genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 14
genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 14
genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 14
genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 14
genus_species is Bacillus anthracis PEN I AMX S Bacillus anthracis Breakpoints 14
genus_species is Bacillus anthracis PEN R AMX R Bacillus anthracis Breakpoints 14
genus_species is Bacillus anthracis TCY-S S DOX S Bacillus anthracis Breakpoints 14
genus_species is Bacillus anthracis TCY-S R DOX R Bacillus anthracis Breakpoints 14
genus_species is Brucella melitensis TCY-S S DOX S Brucella melitensis Breakpoints 14
genus_species is Brucella melitensis TCY-S R DOX R Brucella melitensis Breakpoints 14
genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 14
genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 14
order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1

Can't render this file because it has a wrong number of fields in line 9.

38
data-raw/gpt_training_text_v2.1.1.9197.txt → data-raw/gpt_training_text_v2.1.1.9198.txt
View File

@ -1,6 +1,6 @@
This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
First and foremost, you are trained on version 2.1.1.9197. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9198. Remember this whenever someone asks which AMR package version you’re at.
Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens.
----------------------------------------------------------------------------------------------------
@ -732,7 +732,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/AMR-deprecated.Rd':
\alias{ab_selector}
\title{Deprecated Functions}
\format{
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 495 rows and 14 columns.
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 496 rows and 14 columns.
}
\usage{
ab_class(...)
@ -2164,13 +2164,15 @@ betalactams_with_inhibitor(only_sir_columns = FALSE, return_all = TRUE,
carbapenems(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins_1st(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_2nd(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_3rd(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_3rd(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins_4th(only_sir_columns = FALSE, return_all = TRUE, ...)
@ -2283,13 +2285,13 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) 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/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/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]{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/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/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/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/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]{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/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[=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/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_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/nacubactam (FNC), 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)
@ -2503,9 +2505,9 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/antimicrobials.Rd':
\name{antimicrobials}
\alias{antimicrobials}
\alias{antivirals}
\title{Data Sets with 615 Antimicrobial Drugs}
\title{Data Sets with 616 Antimicrobial Drugs}
\format{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 495 observations and 14 variables:}{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 496 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr antimcrobial 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.}}
@ -4179,6 +4181,8 @@ The default is \code{"human"}, which can also be set with the package option \co
\subsection{Imported from WHONET}{
Clinical breakpoints in this package were validated through and imported from \href{https://whonet.org}{WHONET}, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on \href{https://whonet.org}{their website}. The developers of WHONET and this \code{AMR} package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.
Our import and reproduction script can be found here: \url{https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_clinical_breakpoints.R}.
}
\subsection{Response from CLSI and EUCAST}{
@ -4505,16 +4509,16 @@ These 34 antimicrobial groups are allowed in the rules (case-insensitive) and ca
\item aminopenicillins\cr(amoxicillin 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/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, 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\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/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/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/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, 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\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/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 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/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_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/nacubactam, 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/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, 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/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 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)
@ -4631,9 +4635,9 @@ 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", "expert")),
verbose = FALSE, version_breakpoints = 12, version_expertrules = 3.3,
verbose = FALSE, version_breakpoints = 14, version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA, only_sir_columns = FALSE,
custom_rules = NULL, overwrite = TRUE, ...)
custom_rules = NULL, overwrite = FALSE, ...)
eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
}
@ -4648,7 +4652,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
\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.}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be "12.0", "11.0", or "10.0".}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be "14.0", "13.1", "12.0", "11.0", or "10.0".}
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".}
@ -4658,7 +4662,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
\item{custom_rules}{custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}}
\item{overwrite}{a \link{logical} to indicate whether non-\code{NA} values must be overwritten (defaults to \code{TRUE}). With \code{FALSE}, only \code{NA} values are changed.}
\item{overwrite}{A \link{logical} indicating whether to overwrite non-\code{NA} values (default: \code{FALSE}). When \code{FALSE}, only \code{NA} values are modified. To ensure compliance with EUCAST guidelines, \strong{this should remain} \code{FALSE}, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant."}
\item{...}{column name of an antimicrobial, see section \emph{Antimicrobials} below}

1
data-raw/reproduction_of_antimicrobials.R
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@ -1060,3 +1060,4 @@ for (i in 1:nrow(antimicrobials)) {
usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")
rm(antimicrobials)
devtools::load_all(".")

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data/antimicrobials.rda
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2
man/AMR-deprecated.Rd
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@ -8,7 +8,7 @@
\alias{ab_selector}
\title{Deprecated Functions}
\format{
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 495 rows and 14 columns.
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 496 rows and 14 columns.
}
\usage{
ab_class(...)

12
man/antimicrobial_selectors.Rd
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@ -58,13 +58,15 @@ betalactams_with_inhibitor(only_sir_columns = FALSE, return_all = TRUE,
carbapenems(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins_1st(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_2nd(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_3rd(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_3rd(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins_4th(only_sir_columns = FALSE, return_all = TRUE, ...)
@ -177,13 +179,13 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) 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/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/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]{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/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/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/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/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]{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/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[=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/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_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/nacubactam (FNC), 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)

4
man/antimicrobials.Rd
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@ -4,9 +4,9 @@
\name{antimicrobials}
\alias{antimicrobials}
\alias{antivirals}
\title{Data Sets with 615 Antimicrobial Drugs}
\title{Data Sets with 616 Antimicrobial Drugs}
\format{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 495 observations and 14 variables:}{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 496 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr antimcrobial 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.}}

2
man/clinical_breakpoints.Rd
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@ -49,6 +49,8 @@ The default is \code{"human"}, which can also be set with the package option \co
\subsection{Imported from WHONET}{
Clinical breakpoints in this package were validated through and imported from \href{https://whonet.org}{WHONET}, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on \href{https://whonet.org}{their website}. The developers of WHONET and this \code{AMR} package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.
Our import and reproduction script can be found here: \url{https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_clinical_breakpoints.R}.
}
\subsection{Response from CLSI and EUCAST}{

8
man/custom_eucast_rules.Rd
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@ -92,16 +92,16 @@ These 34 antimicrobial groups are allowed in the rules (case-insensitive) and ca
\item aminopenicillins\cr(amoxicillin 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/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, 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\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/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/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/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, 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\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/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 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/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_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/nacubactam, 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/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, 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/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 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)

8
man/eucast_rules.Rd
View File

@ -21,9 +21,9 @@ 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", "expert")),
verbose = FALSE, version_breakpoints = 12, version_expertrules = 3.3,
verbose = FALSE, version_breakpoints = 14, version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA, only_sir_columns = FALSE,
custom_rules = NULL, overwrite = TRUE, ...)
custom_rules = NULL, overwrite = FALSE, ...)
eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
}
@ -38,7 +38,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
\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.}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be "12.0", "11.0", or "10.0".}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be "14.0", "13.1", "12.0", "11.0", or "10.0".}
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".}
@ -48,7 +48,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
\item{custom_rules}{custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}}
\item{overwrite}{a \link{logical} to indicate whether non-\code{NA} values must be overwritten (defaults to \code{TRUE}). With \code{FALSE}, only \code{NA} values are changed.}
\item{overwrite}{A \link{logical} indicating whether to overwrite non-\code{NA} values (default: \code{FALSE}). When \code{FALSE}, only \code{NA} values are modified. To ensure compliance with EUCAST guidelines, \strong{this should remain} \code{FALSE}, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant."}
\item{...}{column name of an antimicrobial, see section \emph{Antimicrobials} below}