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AMR/man/eucast_rules.Rd

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/eucast_rules.R
\name{eucast_rules}
\alias{eucast_rules}
\alias{EUCAST}
\alias{eucast_dosage}
\title{Apply EUCAST Rules}
\source{
\itemize{
\item EUCAST Expert Rules. Version 2.0, 2012.\cr
Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
\item EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{(link)}
\item EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{(link)}
\item EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx}{(link)}
}
}
\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,
ampc_cephalosporin_resistance = NA,
only_sir_columns = FALSE,
custom_rules = NULL,
...
)
eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
}
\arguments{
\item{x}{a data set with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{info}{a \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions}
\item{rules}{a \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value using the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_eucastrules}}: \code{options(AMR_eucastrules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
\item{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_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".}
\item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these version of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia}, and \emph{Serratia}.}
\item{only_sir_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE})}
\item{custom_rules}{custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}}
\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
\item{administration}{route of administration, either "im", "iv", or "oral"}
}
\value{
The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.
}
\description{
Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://www.eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get a \link{data.frame} with advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see \emph{Details}.
}
\details{
\strong{Note:} This function does not translate MIC values to SIR values. Use \code{\link[=as.sir]{as.sir()}} for that. \cr
\strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until June 24th, 2024, see \link{microorganisms}.
\subsection{Custom Rules}{
Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
eucast_rules(example_isolates, rules = "custom", custom_rules = x)
}\if{html}{\out{</div>}}
}
\subsection{'Other' Rules}{
Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:
\enumerate{
\item A drug \strong{with} enzyme inhibitor will be set to S if the same drug \strong{without} enzyme inhibitor is S
\item A drug \strong{without} enzyme inhibitor will be set to R if the same drug \strong{with} enzyme inhibitor is R
}
Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_eucastrules}}, i.e. run \code{options(AMR_eucastrules = "all")}.
}
}
\section{Antibiotics}{
To define antibiotics column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
The following antibiotics are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://atcddd.fhi.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=S01AE08&showdescription=no}{S01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefetamet (\code{CAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD10&showdescription=no}{J01DD10}), cefixime (\code{CFM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD01&showdescription=no}{J01DD01}), cefotaxime/clavulanic acid (\code{CTC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD51&showdescription=no}{J01DD51}), cefotetan (\code{CTT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC07&showdescription=no}{J01DC07}), cefovecin (\code{FOV}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01DD91&showdescription=no}{QJ01DD91}), cefoxitin (\code{FOX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC01&showdescription=no}{J01DC01}), cefozopran (\code{ZOP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE03&showdescription=no}{J01DE03}), cefpiramide (\code{CPM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE02&showdescription=no}{J01DE02}), cefpodoxime (\code{CPD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD13&showdescription=no}{J01DD13}), cefprozil (\code{CPR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC10&showdescription=no}{J01DC10}), cefquinome (\code{CEQ}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA07&showdescription=no}{QG51AA07}), cefroxadine (\code{CRD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB11&showdescription=no}{J01DB11}), cefsulodin (\code{CFS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD03&showdescription=no}{J01DD03}), ceftaroline (\code{CPT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI02&showdescription=no}{J01DI02}), ceftazidime (\code{CAZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD02&showdescription=no}{J01DD02}), ceftazidime/clavulanic acid (\code{CCV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD52&showdescription=no}{J01DD52}), cefteram (\code{CEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD18&showdescription=no}{J01DD18}), ceftezole (\code{CTL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB12&showdescription=no}{J01DB12}), ceftibuten (\code{CTB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD14&showdescription=no}{J01DD14}), ceftiofur (\code{TIO}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01DD90&showdescription=no}{QJ01DD90}), ceftizoxime (\code{CZX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD07&showdescription=no}{J01DD07}), ceftobiprole medocaril (\code{CFM1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI01&showdescription=no}{J01DI01}), ceftolozane/tazobactam (\code{CZT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI54&showdescription=no}{J01DI54}), ceftriaxone (\code{CRO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD04&showdescription=no}{J01DD04}), ceftriaxone/beta-lactamase inhibitor (\code{CEB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD63&showdescription=no}{J01DD63}), cefuroxime (\code{CXM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC02&showdescription=no}{J01DC02}), cephradine (\code{CED}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB09&showdescription=no}{J01DB09}), chloramphenicol (\code{CHL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01BA01&showdescription=no}{J01BA01}), ciprofloxacin (\code{CIP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA02&showdescription=no}{J01MA02}), clarithromycin (\code{CLR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA09&showdescription=no}{J01FA09}), clindamycin (\code{CLI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FF01&showdescription=no}{J01FF01}), clometocillin (\code{CLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE07&showdescription=no}{J01CE07}), cloxacillin (\code{CLO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF02&showdescription=no}{J01CF02}), colistin (\code{COL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XB01&showdescription=no}{J01XB01}), cycloserine (\code{CYC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J04AB01&showdescription=no}{J04AB01}), dalbavancin (\code{DAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA04&showdescription=no}{J01XA04}), danofloxacin (\code{DAN}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA92&showdescription=no}{QJ01MA92}), daptomycin (\code{DAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX09&showdescription=no}{J01XX09}), delafloxacin (\code{DFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA23&showdescription=no}{J01MA23}), dibekacin (\code{DKB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB09&showdescription=no}{J01GB09}), dicloxacillin (\code{DIC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF01&showdescription=no}{J01CF01}), difloxacin (\code{DIF}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA94&showdescription=no}{QJ01MA94}), dirithromycin (\code{DIR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA13&showdescription=no}{J01FA13}), doripenem (\code{DOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH04&showdescription=no}{J01DH04}), doxycycline (\code{DOX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA02&showdescription=no}{J01AA02}), enoxacin (\code{ENX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA04&showdescription=no}{J01MA04}), enrofloxacin (\code{ENR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA90&showdescription=no}{QJ01MA90}), epicillin (\code{EPC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA07&showdescription=no}{J01CA07}), ertapenem (\code{ETP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH03&showdescription=no}{J01DH03}), erythromycin (\code{ERY}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA01&showdescription=no}{J01FA01}), fleroxacin (\code{FLE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA08&showdescription=no}{J01MA08}), flucloxacillin (\code{FLC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF05&showdescription=no}{J01CF05}), flurithromycin (\code{FLR1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA14&showdescription=no}{J01FA14}), fosfomycin (\code{FOS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX01&showdescription=no}{J01XX01}), framycetin (\code{FRM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=D09AA01&showdescription=no}{D09AA01}), fusidic acid (\code{FUS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XC01&showdescription=no}{J01XC01}), gamithromycin (\code{GAM}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA95&showdescription=no}{QJ01FA95}), garenoxacin (\code{GRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA19&showdescription=no}{J01MA19}), gatifloxacin (\code{GAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA16&showdescription=no}{J01MA16}), gemifloxacin (\code{GEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA15&showdescription=no}{J01MA15}), gentamicin (\code{GEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB03&showdescription=no}{J01GB03}), grepafloxacin (\code{GRX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA11&showdescription=no}{J01MA11}), hetacillin (\code{HET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA18&showdescription=no}{J01CA18}), imipenem (\code{IPM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH51&showdescription=no}{J01DH51}), imipenem/relebactam (\code{IMR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH56&showdescription=no}{J01DH56}), isepamicin (\code{ISE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB11&showdescription=no}{J01GB11}), josamycin (\code{JOS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA07&showdescription=no}{J01FA07}), kanamycin (\code{KAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB04&showdescription=no}{J01GB04}), kitasamycin (\code{KIT}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA93&showdescription=no}{QJ01FA93}), lascufloxacin (\code{LSC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA25&showdescription=no}{J01MA25}), latamoxef (\code{LTM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD06&showdescription=no}{J01DD06}), levofloxacin (\code{LVX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA12&showdescription=no}{J01MA12}), levonadifloxacin (\code{LND}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA24&showdescription=no}{J01MA24}), lincomycin (\code{LIN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FF02&showdescription=no}{J01FF02}), linezolid (\code{LNZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX08&showdescription=no}{J01XX08}), lomefloxacin (\code{LOM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA07&showdescription=no}{J01MA07}), loracarbef (\code{LOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC08&showdescription=no}{J01DC08}), marbofloxacin (\code{MAR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA93&showdescription=no}{QJ01MA93}), mecillinam (\code{MEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA11&showdescription=no}{J01CA11}), meropenem (\code{MEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH02&showdescription=no}{J01DH02}), meropenem/vaborbactam (\code{MEV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH52&showdescription=no}{J01DH52}), metampicillin (\code{MTM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA14&showdescription=no}{J01CA14}), meticillin (\code{MET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF03&showdescription=no}{J01CF03}), mezlocillin (\code{MEZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA10&showdescription=no}{J01CA10}), micronomicin (\code{MCR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=S01AA22&showdescription=no}{S01AA22}), midecamycin (\code{MID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA03&showdescription=no}{J01FA03}), minocycline (\code{MNO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA08&showdescription=no}{J01AA08}), miocamycin (\code{MCM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA11&showdescription=no}{J01FA11}), moxifloxacin (\code{MFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA14&showdescription=no}{J01MA14}), nadifloxacin (\code{NAD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=D10AF05&showdescription=no}{D10AF05}), nafcillin (\code{NAF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF06&showdescription=no}{J01CF06}), nalidixic acid (\code{NAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MB02&showdescription=no}{J01MB02}), neomycin (\code{NEO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB05&showdescription=no}{J01GB05}), netilmicin (\code{NET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB07&showdescription=no}{J01GB07}), nitrofurantoin (\code{NIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XE01&showdescription=no}{J01XE01}), norfloxacin (\code{NOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA06&showdescription=no}{J01MA06}), novobiocin (\code{NOV}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01XX95&showdescription=no}{QJ01XX95}), ofloxacin (\code{OFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA01&showdescription=no}{J01MA01}), oleandomycin (\code{OLE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA05&showdescription=no}{J01FA05}), orbifloxacin (\code{ORB}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA95&showdescription=no}{QJ01MA95}), oritavancin (\code{ORI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA05&showdescription=no}{J01XA05}), oxacillin (\code{OXA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF04&showdescription=no}{J01CF04}), panipenem (\code{PAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH55&showdescription=no}{J01DH55}), pazufloxacin (\code{PAZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA18&showdescription=no}{J01MA18}), pefloxacin (\code{PEF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA03&showdescription=no}{J01MA03}), penamecillin (\code{PNM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE06&showdescription=no}{J01CE06}), pheneticillin (\code{PHE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE05&showdescription=no}{J01CE05}), phenoxymethylpenicillin (\code{PHN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE02&showdescription=no}{J01CE02}), piperacillin (\code{PIP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA12&showdescription=no}{J01CA12}), piperacillin/tazobactam (\code{TZP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR05&showdescription=no}{J01CR05}), pirlimycin (\code{PRL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ51FF90&showdescription=no}{QJ51FF90}), pivampicillin (\code{PVM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA02&showdescription=no}{J01CA02}), pivmecillinam (\code{PME}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA08&showdescription=no}{J01CA08}), plazomicin (\code{PLZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB14&showdescription=no}{J01GB14}), polymyxin B (\code{PLB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XB02&showdescription=no}{J01XB02}), pradofloxacin (\code{PRA}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA97&showdescription=no}{QJ01MA97}), pristinamycin (\code{PRI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FG01&showdescription=no}{J01FG01}), procaine benzylpenicillin (\code{PRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE09&showdescription=no}{J01CE09}), propicillin (\code{PRP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE03&showdescription=no}{J01CE03}), prulifloxacin (\code{PRU}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA17&showdescription=no}{J01MA17}), quinupristin/dalfopristin (\code{QDA}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FG02&showdescription=no}{QJ01FG02}), ribostamycin (\code{RST}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB10&showdescription=no}{J01GB10}), rifampicin (\code{RIF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J04AB02&showdescription=no}{J04AB02}), rokitamycin (\code{ROK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA12&showdescription=no}{J01FA12}), roxithromycin (\code{RXT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA06&showdescription=no}{J01FA06}), rufloxacin (\code{RFL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA10&showdescription=no}{J01MA10}), sarafloxacin (\code{SAR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA98&showdescription=no}{QJ01MA98}), sisomicin (\code{SIS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB08&showdescription=no}{J01GB08}), sitafloxacin (\code{SIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA21&showdescription=no}{J01MA21}), solithromycin (\code{SOL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA16&showdescription=no}{J01FA16}), sparfloxacin (\code{SPX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA09&showdescription=no}{J01MA09}), spiramycin (\code{SPI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA02&showdescription=no}{J01FA02}), streptoduocin (\code{STR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GA02&showdescription=no}{J01GA02}), streptomycin (\code{STR1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GA01&showdescription=no}{J01GA01}), sulbactam (\code{SUL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CG01&showdescription=no}{J01CG01}), sulbenicillin (\code{SBC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA16&showdescription=no}{J01CA16}), sulfadiazine (\code{SDI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC02&showdescription=no}{J01EC02}), sulfadiazine/trimethoprim (\code{SLT1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE02&showdescription=no}{J01EE02}), sulfadimethoxine (\code{SUD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED01&showdescription=no}{J01ED01}), sulfadimidine (\code{SDM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB03&showdescription=no}{J01EB03}), sulfadimidine/trimethoprim (\code{SLT2}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE05&showdescription=no}{J01EE05}), sulfafurazole (\code{SLF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB05&showdescription=no}{J01EB05}), sulfaisodimidine (\code{SLF1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB01&showdescription=no}{J01EB01}), sulfalene (\code{SLF2}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED02&showdescription=no}{J01ED02}), sulfamazone (\code{SZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED09&showdescription=no}{J01ED09}), sulfamerazine (\code{SLF3}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED07&showdescription=no}{J01ED07}), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE07&showdescription=no}{J01EE07}), sulfamethizole (\code{SLF4}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB02&showdescription=no}{J01EB02}), sulfamethoxazole (\code{SMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC01&showdescription=no}{J01EC01}), sulfamethoxypyridazine (\code{SLF5}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED05&showdescription=no}{J01ED05}), sulfametomidine (\code{SLF6}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED03&showdescription=no}{J01ED03}), sulfametoxydiazine (\code{SLF7}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED04&showdescription=no}{J01ED04}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE03&showdescription=no}{J01EE03}), sulfamoxole (\code{SLF8}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC03&showdescription=no}{J01EC03}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE04&showdescription=no}{J01EE04}), sulfanilamide (\code{SLF9}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB06&showdescription=no}{J01EB06}), sulfaperin (\code{SLF10}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED06&showdescription=no}{J01ED06}), sulfaphenazole (\code{SLF11}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED08&showdescription=no}{J01ED08}), sulfapyridine (\code{SLF12}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB04&showdescription=no}{J01EB04}), sulfathiazole (\code{SUT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB07&showdescription=no}{J01EB07}), sulfathiourea (\code{SLF13}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB08&showdescription=no}{J01EB08}), sultamicillin (\code{SLT6}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR04&showdescription=no}{J01CR04}), talampicillin (\code{TAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA15&showdescription=no}{J01CA15}), tazobactam (\code{TAZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CG02&showdescription=no}{J01CG02}), tebipenem (\code{TBP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH06&showdescription=no}{J01DH06}), tedizolid (\code{TZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX11&showdescription=no}{J01XX11}), teicoplanin (\code{TEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA02&showdescription=no}{J01XA02}), telavancin (\code{TLV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA03&showdescription=no}{J01XA03}), telithromycin (\code{TLT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA15&showdescription=no}{J01FA15}), temafloxacin (\code{TMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA05&showdescription=no}{J01MA05}), temocillin (\code{TEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA17&showdescription=no}{J01CA17}), tetracycline (\code{TCY}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA07&showdescription=no}{J01AA07}), ticarcillin (\code{TIC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA13&showdescription=no}{J01CA13}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR03&showdescription=no}{J01CR03}), tigecycline (\code{TGC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA12&showdescription=no}{J01AA12}), tilbroquinol (\code{TBQ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=P01AA05&showdescription=no}{P01AA05}), tildipirosin (\code{TIP}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA96&showdescription=no}{QJ01FA96}), tilmicosin (\code{TIL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA91&showdescription=no}{QJ01FA91}), tobramycin (\code{TOB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB01&showdescription=no}{J01GB01}), tosufloxacin (\code{TFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA22&showdescription=no}{J01MA22}), trimethoprim (\code{TMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EA01&showdescription=no}{J01EA01}), trimethoprim/sulfamethoxazole (\code{SXT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE01&showdescription=no}{J01EE01}), troleandomycin (\code{TRL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA08&showdescription=no}{J01FA08}), trovafloxacin (\code{TVA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA13&showdescription=no}{J01MA13}), tulathromycin (\code{TUL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA94&showdescription=no}{QJ01FA94}), tylosin (\code{TYL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA90&showdescription=no}{QJ01FA90}), tylvalosin (\code{TYL1}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA92&showdescription=no}{QJ01FA92}), vancomycin (\code{VAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA01&showdescription=no}{J01XA01})
}
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
\donttest{
a <- data.frame(
mo = c(
"Staphylococcus aureus",
"Enterococcus faecalis",
"Escherichia coli",
"Klebsiella pneumoniae",
"Pseudomonas aeruginosa"
),
VAN = "-", # Vancomycin
AMX = "-", # Amoxicillin
COL = "-", # Colistin
CAZ = "-", # Ceftazidime
CXM = "-", # Cefuroxime
PEN = "S", # Benzylpenicillin
FOX = "S", # Cefoxitin
stringsAsFactors = FALSE
)
head(a)
# apply EUCAST rules: some results wil be changed
b <- eucast_rules(a)
head(b)
# do not apply EUCAST rules, but rather get a data.frame
# containing all details about the transformations:
c <- eucast_rules(a, verbose = TRUE)
head(c)
}
# Dosage guidelines:
eucast_dosage(c("tobra", "genta", "cipro"), "iv")
eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
}
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