AMR/man/eucast_rules.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/eucast_rules.R
\name{eucast_rules}
\alias{eucast_rules}
\title{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. \cr
      \url{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.  \cr
      \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
    }
    \item{
      EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
      \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
    }
  }
}
\usage{
eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
  "expert", "other", "all"), verbose = FALSE, ...)
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}

\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}

\item{info}{print progress}

\item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}}

\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.}

\item{...}{column name of an antibiotic, see section Antibiotics}
}
\value{
The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations.
}
\description{
Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
}
\details{
\strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link{as.rsi}} 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.

The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
}
\section{Antibiotics}{

To define antibiotics column names, leave as it is to determine it automatically with \code{\link{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 used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:

 \strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
 \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
 \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
 \strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
 \strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
 \strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
 \strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
 \strong{CAP}: capreomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB30}{J04AB30}),
 \strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
 \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
 \strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
 \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
 \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
 \strong{CED}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
 \strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
 \strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
 \strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
 \strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
 \strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
 \strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
 \strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
 \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
 \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
 \strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
 \strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
 \strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
 \strong{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
 \strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
 \strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
 \strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
 \strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
 \strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
 \strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
 \strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
 \strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
 \strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
 \strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
 \strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
 \strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
 \strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01XD01}{J01XD01}),
 \strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
 \strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
 \strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
 \strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
 \strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
 \strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
 \strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
 \strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
 \strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
 \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
 \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
 \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
 \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
 \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
 \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
 \strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
 \strong{PZA}: pyrazinamide (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK01}{J04AK01}),
 \strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
 \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
 \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
 \strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
 \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
 \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
 \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
 \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
 \strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
 \strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
 \strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
 \strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
 \strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
 \strong{SXT}: trimethoprim/sulfamethoxazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
 \strong{VAN}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
}

\section{Read more on our website!}{

On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}

\examples{
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",       # Penicillin G
                FOX = "S",       # Cefoxitin
                stringsAsFactors = FALSE)

a
#                       mo  VAN  AMX  COL  CAZ  CXM  PEN  FOX
# 1  Staphylococcus aureus    -    -    -    -    -    S    S
# 2  Enterococcus faecalis    -    -    -    -    -    S    S
# 3       Escherichia coli    -    -    -    -    -    S    S
# 4  Klebsiella pneumoniae    -    -    -    -    -    S    S
# 5 Pseudomonas aeruginosa    -    -    -    -    -    S    S


# apply EUCAST rules: 18 results are forced as R or S
b <- eucast_rules(a)

b
#                       mo  VAN  AMX  COL  CAZ  CXM  PEN  FOX
# 1  Staphylococcus aureus    -    S    R    R    S    S    S
# 2  Enterococcus faecalis    -    -    R    R    R    S    R
# 3       Escherichia coli    R    -    -    -    -    R    S
# 4  Klebsiella pneumoniae    R    R    -    -    -    R    S
# 5 Pseudomonas aeruginosa    R    R    -    -    R    R    R


\donttest{
# do not apply EUCAST rules, but rather get a data.frame
# with 18 rows, containing all details about the transformations:
c <- eucast_rules(a, verbose = TRUE)
}
}
\keyword{eucast}
\keyword{interpretive}
\keyword{reading}
\keyword{resistance}