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AMR/man/EUCAST.Rd

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/eucast.R
\name{EUCAST_rules}
\alias{EUCAST_rules}
\alias{interpretive_reading}
\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 8.1, 2018. \cr
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx}
}
}
}
\usage{
EUCAST_rules(tbl, col_mo = "mo", info = TRUE,
rules = c("breakpoints", "expert", "other", "all"), amcl = "amcl",
amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
azlo = "azlo", aztr = "aztr", cefa = "cefa", cfep = "cfep",
cfot = "cfot", cfox = "cfox", cfra = "cfra", cfta = "cfta",
cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
clar = "clar", clin = "clin", clox = "clox", coli = "coli",
czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
imip = "imip", kana = "kana", levo = "levo", linc = "linc",
line = "line", mero = "mero", mezl = "mezl", mino = "mino",
moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
nitr = "nitr", norf = "norf", novo = "novo", oflo = "oflo",
oxac = "oxac", peni = "peni", pita = "pita", poly = "poly",
pris = "pris", qida = "qida", rifa = "rifa", roxi = "roxi",
siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
vanc = "vanc", col_bactid = "bactid", verbose = FALSE)
interpretive_reading(...)
}
\arguments{
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
\item{col_mo}{column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}}
\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{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, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details}
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
\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}
\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 verbose info.
}
\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{
To define antibiotics column names, input a text or use \code{NA} to skip a column (e.g. \code{tica = NA}). Non-existing columns will anyway be skipped with a warning. See the Antibiotics section for an explanation of the abbreviations.
}
\section{Antibiotics}{
Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
\strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}),
\strong{amik}: amikacin (\emph{J01GB06}),
\strong{amox}: amoxicillin (\emph{J01CA04}),
\strong{ampi}: ampicillin (\emph{J01CA01}),
\strong{azit}: azithromycin (\emph{J01FA10}),
\strong{azlo}: azlocillin (\emph{J01CA09}),
\strong{aztr}: aztreonam (\emph{J01DF01}),
\strong{cefa}: cefaloridine (\emph{J01DB02}),
\strong{cfep}: cefepime (\emph{J01DE01}),
\strong{cfot}: cefotaxime (\emph{J01DD01}),
\strong{cfox}: cefoxitin (\emph{J01DC01}),
\strong{cfra}: cefradine (\emph{J01DB09}),
\strong{cfta}: ceftazidime (\emph{J01DD02}),
\strong{cftr}: ceftriaxone (\emph{J01DD04}),
\strong{cfur}: cefuroxime (\emph{J01DC02}),
\strong{chlo}: chloramphenicol (\emph{J01BA01}),
\strong{cipr}: ciprofloxacin (\emph{J01MA02}),
\strong{clar}: clarithromycin (\emph{J01FA09}),
\strong{clin}: clindamycin (\emph{J01FF01}),
\strong{clox}: flucloxacillin (\emph{J01CF05}),
\strong{coli}: colistin (\emph{J01XB01}),
\strong{czol}: cefazolin (\emph{J01DB04}),
\strong{dapt}: daptomycin (\emph{J01XX09}),
\strong{doxy}: doxycycline (\emph{J01AA02}),
\strong{erta}: ertapenem (\emph{J01DH03}),
\strong{eryt}: erythromycin (\emph{J01FA01}),
\strong{fosf}: fosfomycin (\emph{J01XX01}),
\strong{fusi}: fusidic acid (\emph{J01XC01}),
\strong{gent}: gentamicin (\emph{J01GB03}),
\strong{imip}: imipenem (\emph{J01DH51}),
\strong{kana}: kanamycin (\emph{J01GB04}),
\strong{levo}: levofloxacin (\emph{J01MA12}),
\strong{linc}: lincomycin (\emph{J01FF02}),
\strong{line}: linezolid (\emph{J01XX08}),
\strong{mero}: meropenem (\emph{J01DH02}),
\strong{mezl}: mezlocillin (\emph{J01CA10}),
\strong{mino}: minocycline (\emph{J01AA08}),
\strong{moxi}: moxifloxacin (\emph{J01MA14}),
\strong{nali}: nalidixic acid (\emph{J01MB02}),
\strong{neom}: neomycin (\emph{J01GB05}),
\strong{neti}: netilmicin (\emph{J01GB07}),
\strong{nitr}: nitrofurantoin (\emph{J01XE01}),
\strong{norf}: norfloxacin (\emph{J01MA06}),
\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
\strong{oflo}: ofloxacin (\emph{J01MA01}),
\strong{peni}: penicillin (\emph{J01RA01}),
\strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
\strong{poly}: polymyxin B (\emph{J01XB02}),
\strong{pris}: pristinamycin (\emph{J01FG01}),
\strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
\strong{rifa}: rifampicin (\emph{J04AB02}),
\strong{roxi}: roxithromycin (\emph{J01FA06}),
\strong{siso}: sisomicin (\emph{J01GB08}),
\strong{teic}: teicoplanin (\emph{J01XA02}),
\strong{tetr}: tetracycline (\emph{J01AA07}),
\strong{tica}: ticarcillin (\emph{J01CA13}),
\strong{tige}: tigecycline (\emph{J01AA12}),
\strong{tobr}: tobramycin (\emph{J01GB01}),
\strong{trim}: trimethoprim (\emph{J01EA01}),
\strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
\strong{vanc}: vancomycin (\emph{J01XA01}).
}
\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
b <- EUCAST_rules(a) # 18 results are forced as R or S
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
}
\keyword{eucast}
\keyword{interpretive}
\keyword{reading}
\keyword{resistance}
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