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}
\alias{eucast_rules_file}
\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}
    }
  }

  For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: \code{"amcl, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).
}
\usage{
eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
  "expert", "other", "all"), verbose = FALSE, amcl = guess_ab_col(),
  amik = guess_ab_col(), amox = guess_ab_col(),
  ampi = guess_ab_col(), azit = guess_ab_col(),
  azlo = guess_ab_col(), aztr = guess_ab_col(),
  cefa = guess_ab_col(), cfep = guess_ab_col(),
  cfot = guess_ab_col(), cfox = guess_ab_col(),
  cfra = guess_ab_col(), cfta = guess_ab_col(),
  cftr = guess_ab_col(), cfur = guess_ab_col(),
  chlo = guess_ab_col(), cipr = guess_ab_col(),
  clar = guess_ab_col(), clin = guess_ab_col(),
  clox = guess_ab_col(), coli = guess_ab_col(),
  czol = guess_ab_col(), dapt = guess_ab_col(),
  doxy = guess_ab_col(), erta = guess_ab_col(),
  eryt = guess_ab_col(), fosf = guess_ab_col(),
  fusi = guess_ab_col(), gent = guess_ab_col(),
  imip = guess_ab_col(), kana = guess_ab_col(),
  levo = guess_ab_col(), linc = guess_ab_col(),
  line = guess_ab_col(), mero = guess_ab_col(),
  mezl = guess_ab_col(), mino = guess_ab_col(),
  moxi = guess_ab_col(), nali = guess_ab_col(),
  neom = guess_ab_col(), neti = guess_ab_col(),
  nitr = guess_ab_col(), norf = guess_ab_col(),
  novo = guess_ab_col(), oflo = guess_ab_col(),
  oxac = guess_ab_col(), peni = guess_ab_col(),
  pipe = guess_ab_col(), pita = guess_ab_col(),
  poly = guess_ab_col(), pris = guess_ab_col(),
  qida = guess_ab_col(), rifa = guess_ab_col(),
  roxi = guess_ab_col(), siso = guess_ab_col(),
  teic = guess_ab_col(), tetr = guess_ab_col(),
  tica = guess_ab_col(), tige = guess_ab_col(),
  tobr = guess_ab_col(), trim = guess_ab_col(),
  trsu = guess_ab_col(), vanc = guess_ab_col(), ...)

eucast_rules_file()
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{amox} and \code{amcl}}

\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 indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected. It runs all EUCAST rules, but will not be applied to an output - only an informative \code{data.frame} with changes will be returned as output.}

\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Antibiotics}

\item{...}{parameters that are passed on to \code{eucast_rules}}
}
\value{
The input of \code{tbl_}, 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{
The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: \cr
\code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets).

In the source code it is located under \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{\code{./inst/eucast/eucast_rules.tsv}}.

\strong{Note:} When ampicillin (J01CA01) is not available but amoxicillin (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.
}
\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{tica = NULL}). Non-existing columns will anyway be skipped with a warning.

Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})

 \strong{amcl}: amoxicillin+clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
 \strong{amik}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
 \strong{amox}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
 \strong{ampi}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
 \strong{azit}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
 \strong{azlo}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
 \strong{aztr}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
 \strong{cefa}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
 \strong{cfep}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
 \strong{cfot}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
 \strong{cfox}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
 \strong{cfra}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
 \strong{cfta}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
 \strong{cftr}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
 \strong{cfur}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
 \strong{chlo}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
 \strong{cipr}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
 \strong{clar}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
 \strong{clin}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
 \strong{clox}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
 \strong{coli}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
 \strong{czol}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
 \strong{dapt}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
 \strong{doxy}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
 \strong{erta}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
 \strong{eryt}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
 \strong{fosf}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
 \strong{fusi}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
 \strong{gent}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
 \strong{imip}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
 \strong{kana}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
 \strong{levo}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
 \strong{linc}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
 \strong{line}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
 \strong{mero}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
 \strong{mezl}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
 \strong{mino}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
 \strong{moxi}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
 \strong{nali}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
 \strong{neom}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
 \strong{neti}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
 \strong{nitr}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
 \strong{norf}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
 \strong{novo}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
 \strong{oflo}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
 \strong{peni}: (benzyl)penicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
 \strong{pipe}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
 \strong{pita}: piperacillin+tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
 \strong{poly}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
 \strong{pris}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
 \strong{qida}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
 \strong{rifa}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
 \strong{roxi}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
 \strong{siso}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
 \strong{teic}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
 \strong{tetr}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
 \strong{tica}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
 \strong{tige}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
 \strong{tobr}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
 \strong{trim}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
 \strong{trsu}: sulfamethoxazole and trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
 \strong{vanc}: 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 comprehensive 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 <- eucast_rules(septic_patients)

a <- data.frame(mo = c("Staphylococcus aureus",
                       "Enterococcus faecalis",
                       "Escherichia coli",
                       "Klebsiella pneumoniae",
                       "Pseudomonas aeruginosa"),
                vanc = "-",       # Vancomycin
                amox = "-",       # Amoxicillin
                coli = "-",       # Colistin
                cfta = "-",       # Ceftazidime
                cfur = "-",       # Cefuroxime
                peni = "S",       # Benzylpenicillin
                cfox = "S",       # Cefoxitin
                stringsAsFactors = FALSE)

a
#                       mo vanc amox coli cfta cfur peni cfox
# 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 vanc amox coli cfta cfur peni cfox
# 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


# do not apply EUCAST rules, but rather get a 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}