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Changelog

Source: NEWS.md

AMR 1.8.2.9063

(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)

This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.

TL;DR

  • Microbiological taxonomy (microorganisms data set) updated to 2022 and now based on LPSN and GBIF
  • Much increased algorithms to translate user input to valid taxonomy
  • Clinical breakpoints added for EUCAST 2022 and CLSI 2022
  • 20 new antibiotics added and updated all DDDs and ATC codes
  • Extended support for antiviral agents (antivirals data set), with many new functions
  • Now available in 16 languages
  • Many new interesting functions, such as rsi_confidence_interval() and mean_amr_distance()
  • Hundreds of bug fixes

New

Interpretation of MIC and disk diffusion values

EUCAST 2022 and CLSI 2022 guidelines have been added for as.rsi(). EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for eucast_rules() to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new AMR_guideline option, such as: options(AMR_guideline = "CLSI 2020").

Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.

Supported languages

We added support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user system language.

We are very grateful for the valuable input by our colleagues from other countries. The AMR package is now available in 16 languages and according to download stats used in almost all countries in the world!

Microbiological taxonomy

The microorganisms no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.

We also made the following changes regarding the included taxonomy or microorganisms functions: * Updated full microbiological taxonomy according to the latest daily LPSN data set (December 2022) and latest yearly GBIF taxonomy backbone (November 2022) * Support for all 1,515 city-like serovars of Salmonella, such as Salmonella Goldcoast. Formally, these are serovars belonging to the S. enterica species, but they are reported with only the name of the genus and the city. For this reason, the serovars are in the subspecies column of the microorganisms data set and “enterica” is in the species column, but the full name does not contain the species name (enterica). * All new algorithm for as.mo() (and thus all mo_*() functions) while still following our original set-up as described in our recently published JSS paper (DOI 10.18637/jss.v104.i03). * A new argument keep_synonyms allows to not correct for updated taxonomy, in favour of the now deleted argument allow_uncertain * It has increased tremendously in speed and returns generally more consequent results * Sequential coercion is now extremely fast as results are stored to the package environment, although coercion of unknown values must be run once per session. Previous results can be reset/removed with the new mo_reset_session() function. * Support for microorganism codes of the ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net) * The MO matching score algorithm (mo_matching_score()) now counts deletions and substitutions as 2 instead of 1, which impacts the outcome of as.mo() and any mo_*() function * Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons: * CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them * Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package * Chromista are almost never clinically relevant, thus lacking the secondary scope of this package * The microorganisms.old data set was removed, and all previously accepted names are now included in the microorganisms data set. A new column status contains "accepted" for currently accepted names and "synonym" for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.

Antibiotic agents and selectors

The new function add_custom_antimicrobials() allows users to add custom antimicrobial codes and names to the AMR package.

The antibiotics data set was greatly updated: * The following 20 antibiotics have been added (also includes the new J01RA ATC group): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT) * Added some missing ATC codes * Updated DDDs and PubChem Compound IDs * Updated some antibiotic name spelling, now used by WHOCC (such as cephalexin -> cefalexin, and phenethicillin -> pheneticillin) * Antibiotic code “CEI” for ceftolozane/tazobactam has been replaced with “CZT” to comply with EARS-Net and WHONET 2022. The old code will still work in all cases when using as.ab() or any of the ab_*() functions. * Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code B_ANAER to the microorganisms data set and adding the breakpoints of anaerobics to the rsi_interpretation data set, which is used by as.rsi() for interpretion of MIC and disk diffusion values

Also, we added support for using antibiotic selectors in scoped dplyr verbs (with or without using vars()), such as in: ... %>% summarise_at(aminoglycosides(), resistance), please see resistance() for examples.

Antiviral agents

We now added extensive support for antiviral agents! For the first time, the AMR package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.

  • The antivirals data set has been extended with 18 new drugs (also from the new J05AJ ATC group) and now also contains antiviral identifiers and LOINC codes
  • A new data type av (antivirals) has been added, which is functionally similar to ab for antibiotics
  • Functions as.av(), av_name(), av_atc(), av_synonyms(), av_from_text() have all been added as siblings to their ab_*() equivalents
Other new functions
  • Function rsi_confidence_interval() to add confidence intervals in AMR calculation. This is now also included in rsi_df() and proportion_df().
  • Function mean_amr_distance() to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.
  • Function rsi_interpretation_history() to view the history of previous runs of as.rsi(). This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which as.rsi() was run.
  • Function mo_current() to get the currently valid taxonomic name of a microorganism
  • Function add_custom_antimicrobials() to add custom antimicrobial codes and names to the AMR package

Changes

  • Argument combine_IR has been removed from this package (affecting functions count_df(), proportion_df(), and rsi_df() and some plotting functions), since it was replaced with combine_SI three years ago
  • Using units in ab_ddd(..., units = "...") had been deprecated for some time and is now not supported anymore. Use ab_ddd_units() instead.
  • Support for data.frame-enhancing R packages, more specifically: data.table::data.table, janitor::tabyl, tibble::tibble, and tsibble::tsibble. AMR package functions that have a data set as output (such as rsi_df() and bug_drug_combinations()), will now return the same data type as the input.
  • All data sets in this package are now a tibble, instead of base R data.frames. Older R versions are still supported, even if they do not support tibbles.
  • Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info in this article on our website.
  • For as.rsi():
    • Fixed certain EUCAST breakpoints for MIC values
    • Allow NA values (e.g. as.rsi(as.disk(NA), ...))
    • Fix for bug-drug combinations with multiple breakpoints for different body sites
    • Interpretation from MIC and disk zones is now more informative about availability of breakpoints and more robust
  • Removed the as.integer() method for MIC values, since MIC are not integer values and running table() on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally as.integer() on factors work)
  • Fixed determination of Gram stains (mo_gramstain()), since the taxonomic phyla Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes have been renamed to respectively Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota in 2021
  • droplevels() on MIC will now return a common factor at default and will lose the mic class. Use droplevels(..., as.mic = TRUE) to keep the mic class.
  • Small fix for using ab_from_text()
  • Fixes for reading in text files using set_mo_source(), which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
  • Fixed a bug for mdro() when using similar column names with the Magiorakos guideline
  • Using any random_*() function (such as random_mic()) is now possible by directly calling the package without loading it first: AMR::random_mic(10)
  • Extended support for the vctrs package, used internally by the tidyverse. This allows to change values of class mic, disk, rsi, mo and ab in tibbles, and to use antibiotic selectors for selecting/filtering, e.g. df[carbapenems() == "R", ]
  • Fix for using info = FALSE in mdro()
  • For all interpretation guidelines using as.rsi() on amoxicillin, the rules for ampicillin will be used if amoxicillin rules are not available
  • Fix for using ab_atc() on non-existing ATC codes
  • Black and white message texts are now reversed in colour if using an RStudio dark theme
  • mo_snomed() now returns class character, not numeric anymore (to make long SNOMED codes readable)
  • Fix for using as.ab() on NA values
  • Updated support for all WHONET 2022 microorganism codes
  • Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined by CLSI) will be interpreted as ‘I’ to comply with EUCAST’s ‘I’ in as.rsi()
  • Fix for mo_shortname() in case of higher taxonomic ranks (order, class, phylum)
  • Cleaning columns with as.rsi(), as.mic(), or as.disk() will now show the column name in the warning for invalid results

Other

  • New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions
  • Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input
  • All R and Rmd files in this project are now styled using the styler package
  • Set scalar conditional expressions (&& and ||) where possible to comply with the upcoming R 4.3
  • An enormous lot of code cleaning, fixing some small bugs on the way

AMR 1.8.2

CRAN release: 2022-09-29

This is a small intermediate update to include the reference to our publication in the Journal of Statistical Software, DOI 10.18637/jss.v104.i03.

A major update will be released by the end of 2022 or early 2023 to include the most recent EUCAST and CLSI guidelines, updated microbial taxonomy, and support for 16 languages.

AMR 1.8.1

CRAN release: 2022-03-24

Changed

  • Fix for using as.rsi() on values containing capped values (such as >=), sometimes leading to NA

  • Support for antibiotic interpretations of the MIPS laboratory system: "U" for S (‘susceptible urine’), "D" for I (‘susceptible dose-dependent’)

  • Improved algorithm of as.mo(), especially for ignoring non-taxonomic text, such as:

    
mo_name("methicillin-resistant S. aureus (MRSA)")
#> [1] "Staphylococcus aureus"

  • More informative warning messages

  • Added 192 as valid MIC

  • Updated MIC printing in tibbles

  • Increased speed for loading the package

Other

  • Fix for unit testing on R 3.3
  • Fix for size of some image elements, as requested by CRAN

AMR 1.8.0

CRAN release: 2022-01-07

Breaking changes

  • Removed p_symbol() and all filter_*() functions (except for filter_first_isolate()), which were all deprecated in a previous package version
  • Removed the key_antibiotics() and key_antibiotics_equal() functions, which were deprecated and superseded by key_antimicrobials() and antimicrobials_equal()
  • Removed all previously implemented ggplot2::ggplot() generics for classes <mic>, <disk>, <rsi> and <resistance_predict> as they did not follow the ggplot2 logic. They were replaced with ggplot2::autoplot() generics.
  • Renamed function get_locale() to get_AMR_locale() to prevent conflicts with other packages

New

  • Support for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the rsi_translation data set. This data set now more strictly follows the WHONET software as well.

  • Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for eucast_rules(), mo_is_intrinsic_resistant() and mdro(). The intrinsic_resistant data set was also updated accordingly.

  • Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish

  • Function set_ab_names() to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:

    
example_isolates %>% set_ab_names(where(is.rsi))
example_isolates %>% set_ab_names(AMC:GEN, property = "atc")

  • Function mo_lpsn() to retrieve the LPSN record ID

  • Function ab_ddd_units() to get units of DDDs (daily defined doses), deprecating the use of ab_ddd(..., units = TRUE) to be more consistent in data types of function output

Changed

  • Updated the bacterial taxonomy to 5 October 2021 (according to LPSN), including all 11 new staphylococcal species named since 1 January last year
  • The antibiotics data set now contains all ATC codes that are available through the WHOCC website, regardless of drugs being present in more than one ATC group. This means that:
    • Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
    • antibiotics$atc is now a list containing character vectors, and this atc column was moved to the 5th position of the antibiotics data set
    • ab_atc() does not always return a character vector of length 1, and returns a list if the input is larger than length 1
    • ab_info() has a slightly different output
    • Some DDDs (daily defined doses) were added or updated according to newly included ATC codes
  • Antibiotic selectors

    • They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 like the rest of the package

    • Added more selectors for antibiotic classes: aminopenicillins(), antifungals(), antimycobacterials(), lincosamides(), lipoglycopeptides(), polymyxins(), quinolones(), streptogramins(), trimethoprims() and ureidopenicillins()

    • Added specific selectors for certain types for treatment: administrable_per_os() and administrable_iv(), which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):

      
example_isolates[, penicillins() & administrable_per_os()]          # base R
example_isolates %>% select(penicillins() & administrable_per_os()) # dplyr

    • Added the selector ab_selector(), which accepts a filter to be used internally on the antibiotics data set, yielding great flexibility on drug properties, such as selecting antibiotic columns with an oral DDD of at least 1 gram:

      
example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]          # base R
example_isolates %>% select(ab_selector(oral_ddd > 1 & oral_units == "g")) # dplyr

    • Added the selector not_intrinsic_resistant(), which only keeps antibiotic columns that are not intrinsic resistant for all microorganisms in a data set, based on the latest EUCAST guideline on intrinsic resistance. For example, if a data set contains only microorganism codes or names of E. coli and K. pneumoniae and contains a column “vancomycin”, this column will be removed (or rather, unselected) using this function.

    • Added argument only_treatable, which defaults to TRUE and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)

    • Fix for using selectors multiple times in one call (e.g., using them in dplyr::filter() and immediately after in dplyr::select())

    • Fix for using having multiple columns that are coerced to the same antibiotic agent

    • Fixed for using all() or any() on antibiotic selectors in an R Markdown file

  • Added the following antimicrobial agents that are now covered by the WHO: aztreonam/nacubactam (ANC), cefepime/nacubactam (FNC), exebacase (EXE), ozenoxacin (OZN), zoliflodacin (ZFD), manogepix (MGX), ibrexafungerp (IBX), and rezafungin (RZF). None of these agents have an ATC code yet.
  • Fixed the Gram stain (mo_gramstain()) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as Negativicoccus and Veillonella.
  • Dramatic speed improvement for first_isolate()
  • Fix to prevent introducing NAs for old MO codes when running as.mo() on them
  • Added more informative error messages when any of the proportion_*() and count_*() functions fail
  • When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using as.mo()
  • Improved automatic column selector when col_* arguments are left blank, e.g. in first_isolate()
  • The right input types for random_mic(), random_disk() and random_rsi() are now enforced
  • as.rsi() has an improved algorithm and can now also correct for textual input (such as “Susceptible”, “Resistant”) in all supported languages
  • as.mic() has an improved algorithm
  • When warnings are thrown because of too few isolates in any count_*(), proportion_*() function (or resistant() or susceptible()), the dplyr group will be shown, if available
  • Fix for legends created with scale_rsi_colours() when using ggplot2 v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)
  • Fix for minor translation errors
  • Fix for the MIC interpretation of Morganellaceae (such as Morganella and Proteus) when using the EUCAST 2021 guideline
  • Improved algorithm of as.mo()
  • Improved algorithm for generating random MICs with random_mic()
  • Improved plot legends for MICs and disk diffusion values
  • Improved speed of as.ab() and all ab_*() functions
  • Added fortify() extensions for plotting methods
  • NA values of the classes <mic>, <disk> and <rsi> are now exported objects of this package, e.g. NA_mic_ is an NA of class mic (just like the base R NA_character_ is an NA of class character)
  • The proportion_df(), count_df() and rsi_df() functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packages
  • The mdro() function now returns NA for all rows that have no test results
  • The species_id column in the microorganisms data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and mo_url() has been updated to reflect this change.
  • Fixed a small bug in the functions get_episode() and is_new_episode()
  • get_episode() and is_new_episode() can now cope with NAs

Other

  • This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations.