% 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 AMC. They can be separated by comma: \code{"AMC, 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, ...) eucast_rules_file() } \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 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{...}{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 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 \code{eucast_rules()} can be found by running this command: \cr \code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets). In the source code the file containing all rules is located \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{here}. } \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. Available abbrevations of the column containing antibiotics in the form '\strong{antimicrobial ID}: name (\emph{ATC code})': \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}), \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{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{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}), \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{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}), \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}), \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}), \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{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{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{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{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{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01XD01}), \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=J01MA01}{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{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}), \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}), \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 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"), 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 # 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}