mirror of https://github.com/msberends/AMR.git
733 lines
29 KiB
R
Executable File
733 lines
29 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' EUCAST expert rules
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#'
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#' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
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#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
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#' @param col_bactid column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$bactid}, see \code{\link{microorganisms}}
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#' @param info print progress
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#' @param 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,peni,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column names of antibiotics. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.
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#' @param ... parameters that are passed on to \code{EUCAST_rules}
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#' @section Abbrevations of antibiotics:
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#' Abbrevations of the column containing antibiotics:
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#'
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#' \strong{amcl}: amoxicillin and beta-lactamase inhibitor (\emph{J01CR02}),
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#' \strong{amik}: amikacin (\emph{J01GB06}),
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#' \strong{amox}: amoxicillin (\emph{J01CA04}),
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#' \strong{ampi}: ampicillin (\emph{J01CA01}),
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#' \strong{azit}: azithromycin (\emph{J01FA10}),
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#' \strong{azlo}: azlocillin (\emph{J01CA09}),
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#' \strong{aztr}: aztreonam (\emph{J01DF01}),
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#' \strong{cefa}: cefaloridine (\emph{J01DB02}),
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#' \strong{cfep}: cefepime (\emph{J01DE01}),
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#' \strong{cfot}: cefotaxime (\emph{J01DD01}),
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#' \strong{cfox}: cefoxitin (\emph{J01DC01}),
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#' \strong{cfra}: cefradine (\emph{J01DB09}),
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#' \strong{cfta}: ceftazidime (\emph{J01DD02}),
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#' \strong{cftr}: ceftriaxone (\emph{J01DD04}),
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#' \strong{cfur}: cefuroxime (\emph{J01DC02}),
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#' \strong{chlo}: chloramphenicol (\emph{J01BA01}),
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#' \strong{cipr}: ciprofloxacin (\emph{J01MA02}),
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#' \strong{clar}: clarithromycin (\emph{J01FA09}),
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#' \strong{clin}: clindamycin (\emph{J01FF01}),
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#' \strong{clox}: flucloxacillin (\emph{J01CF05}),
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#' \strong{coli}: colistin (\emph{J01XB01}),
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#' \strong{czol}: cefazolin (\emph{J01DB04}),
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#' \strong{dapt}: daptomycin (\emph{J01XX09}),
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#' \strong{doxy}: doxycycline (\emph{J01AA02}),
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#' \strong{erta}: ertapenem (\emph{J01DH03}),
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#' \strong{eryt}: erythromycin (\emph{J01FA01}),
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#' \strong{fosf}: fosfomycin (\emph{J01XX01}),
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#' \strong{fusi}: fusidic acid (\emph{J01XC01}),
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#' \strong{gent}: gentamicin (\emph{J01GB03}),
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#' \strong{imip}: imipenem and cilastatin (\emph{J01DH51}),
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#' \strong{kana}: kanamycin (\emph{J01GB04}),
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#' \strong{levo}: levofloxacin (\emph{J01MA12}),
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#' \strong{linc}: lincomycin (\emph{J01FF02}),
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#' \strong{line}: linezolid (\emph{J01XX08}),
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#' \strong{mero}: meropenem (\emph{J01DH02}),
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#' \strong{mezl}: mezlocillin (\emph{J01CA10}),
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#' \strong{mino}: minocycline (\emph{J01AA08}),
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#' \strong{moxi}: moxifloxacin (\emph{J01MA14}),
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#' \strong{nali}: nalidixic acid (\emph{J01MB02}),
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#' \strong{neom}: neomycin (\emph{J01GB05}),
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#' \strong{neti}: netilmicin (\emph{J01GB07}),
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#' \strong{nitr}: nitrofurantoin (\emph{J01XE01}),
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#' \strong{norf}: norfloxacin (\emph{J01MA06}),
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#' \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
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#' \strong{oflo}: ofloxacin (\emph{J01MA01}),
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#' \strong{peni}: penicillins, combinations with other antibacterials (\emph{J01RA01}),
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#' \strong{pita}: piperacillin and beta-lactamase inhibitor (\emph{J01CR05}),
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#' \strong{poly}: polymyxin B (\emph{J01XB02}),
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#' \strong{pris}: pristinamycin (\emph{J01FG01}),
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#' \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
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#' \strong{rifa}: rifampicin (\emph{J04AB02}),
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#' \strong{roxi}: roxithromycin (\emph{J01FA06}),
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#' \strong{siso}: sisomicin (\emph{J01GB08}),
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#' \strong{teic}: teicoplanin (\emph{J01XA02}),
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#' \strong{tetr}: tetracycline (\emph{J01AA07}),
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#' \strong{tica}: ticarcillin (\emph{J01CA13}),
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#' \strong{tige}: tigecycline (\emph{J01AA12}),
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#' \strong{tobr}: tobramycin (\emph{J01GB01}),
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#' \strong{trim}: trimethoprim (\emph{J01EA01}),
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#' \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
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#' \strong{vanc}: vancomycin (\emph{J01XA01}).
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#' @keywords interpretive eucast reading resistance
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#' @rdname EUCAST
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#' @export
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#' @importFrom dplyr %>% left_join select
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#' @return table with edited variables of antibiotics.
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#' @source
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#' EUCAST Expert Rules Version 2.0: \cr
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#' Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
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#' \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x} \cr
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#' \cr
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#' EUCAST Expert Rules Version 3.1 (Intrinsic Resistance and Exceptional Phenotypes Tables): \cr
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#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
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#' @examples
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#' a <- EUCAST_rules(septic_patients)
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#' a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
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#' "ENCFAE", # Enterococcus faecalis
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#' "ESCCOL", # Escherichia coli
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#' "KLEPNE", # Klebsiella pneumoniae
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#' "PSEAER"), # Pseudomonas aeruginosa
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#' vanc = "-", # Vancomycin
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#' amox = "-", # Amoxicillin
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#' coli = "-", # Colistin
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#' cfta = "-", # Ceftazidime
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#' cfur = "-", # Cefuroxime
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#' stringsAsFactors = FALSE)
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#' a
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#'
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#' b <- EUCAST_rules(a)
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#' b
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EUCAST_rules <- function(tbl,
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col_bactid = 'bactid',
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info = TRUE,
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amcl = 'amcl',
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amik = 'amik',
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amox = 'amox',
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ampi = 'ampi',
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azit = 'azit',
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azlo = 'azlo',
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aztr = 'aztr',
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cefa = 'cefa',
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cfep = 'cfep',
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cfot = 'cfot',
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cfox = 'cfox',
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cfra = 'cfra',
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cfta = 'cfta',
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cftr = 'cftr',
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cfur = 'cfur',
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chlo = 'chlo',
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cipr = 'cipr',
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clar = 'clar',
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clin = 'clin',
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clox = 'clox',
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coli = 'coli',
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czol = 'czol',
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dapt = 'dapt',
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doxy = 'doxy',
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erta = 'erta',
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eryt = 'eryt',
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fosf = 'fosf',
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fusi = 'fusi',
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gent = 'gent',
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imip = 'imip',
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kana = 'kana',
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levo = 'levo',
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linc = 'linc',
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line = 'line',
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mero = 'mero',
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mezl = 'mezl',
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mino = 'mino',
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moxi = 'moxi',
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nali = 'nali',
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neom = 'neom',
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neti = 'neti',
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nitr = 'nitr',
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norf = 'norf',
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novo = 'novo',
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oflo = 'oflo',
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peni = 'peni',
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pita = 'pita',
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poly = 'poly',
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pris = 'pris',
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qida = 'qida',
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rifa = 'rifa',
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roxi = 'roxi',
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siso = 'siso',
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teic = 'teic',
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tetr = 'tetr',
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tica = 'tica',
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tige = 'tige',
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tobr = 'tobr',
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trim = 'trim',
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trsu = 'trsu',
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vanc = 'vanc') {
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EUCAST_VERSION <- "3.1"
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if (!col_bactid %in% colnames(tbl)) {
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stop('Column ', col_bactid, ' not found.', call. = FALSE)
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}
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# check columns
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col.list <- c(amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot,
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cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
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czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
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levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr,
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novo, norf, oflo, peni, pita, poly, pris, qida, rifa, roxi, siso,
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teic, tetr, tica, tige, tobr, trim, trsu, vanc)
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col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
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amcl <- col.list[amcl]
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amik <- col.list[amik]
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amox <- col.list[amox]
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ampi <- col.list[ampi]
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azit <- col.list[azit]
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azlo <- col.list[azlo]
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aztr <- col.list[aztr]
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cefa <- col.list[cefa]
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cfep <- col.list[cfep]
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cfot <- col.list[cfot]
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cfox <- col.list[cfox]
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cfra <- col.list[cfra]
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cfta <- col.list[cfta]
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cftr <- col.list[cftr]
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cfur <- col.list[cfur]
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chlo <- col.list[chlo]
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cipr <- col.list[cipr]
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clar <- col.list[clar]
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clin <- col.list[clin]
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clox <- col.list[clox]
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coli <- col.list[coli]
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czol <- col.list[czol]
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dapt <- col.list[dapt]
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doxy <- col.list[doxy]
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erta <- col.list[erta]
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eryt <- col.list[eryt]
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fosf <- col.list[fosf]
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fusi <- col.list[fusi]
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gent <- col.list[gent]
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imip <- col.list[imip]
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kana <- col.list[kana]
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levo <- col.list[levo]
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linc <- col.list[linc]
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line <- col.list[line]
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mero <- col.list[mero]
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mezl <- col.list[mezl]
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mino <- col.list[mino]
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moxi <- col.list[moxi]
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nali <- col.list[nali]
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neom <- col.list[neom]
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neti <- col.list[neti]
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nitr <- col.list[nitr]
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norf <- col.list[norf]
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novo <- col.list[novo]
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oflo <- col.list[oflo]
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peni <- col.list[peni]
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pita <- col.list[pita]
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poly <- col.list[poly]
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pris <- col.list[pris]
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qida <- col.list[qida]
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rifa <- col.list[rifa]
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roxi <- col.list[roxi]
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siso <- col.list[siso]
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teic <- col.list[teic]
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tetr <- col.list[tetr]
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tica <- col.list[tica]
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tige <- col.list[tige]
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tobr <- col.list[tobr]
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trim <- col.list[trim]
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trsu <- col.list[trsu]
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vanc <- col.list[vanc]
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total <- 0
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total_rows <- integer(0)
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# helper function for editing the table
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edit_rsi <- function(to, rows, cols, EUCAST_rule = "") {
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# later: use this as attribute for the edited observations
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EUCAST_rule <- trimws(paste("EUCAST rule", EUCAST_rule))
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cols <- cols[!is.na(cols)]
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if (length(rows) > 0 & length(cols) > 0) {
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tbl[rows, cols] <<- to
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total <<- total + (length(rows) * length(cols))
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total_rows <<- c(total_rows, rows)
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}
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}
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# join to microorganisms data set
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if (!tbl %>% pull(col_bactid) %>% is.bactid()) {
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# warning("Improve integrity of the `", col_bactid, "` column by transforming it with 'as.bactid'.")
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}
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tbl <- tbl %>% left_join_microorganisms(by = col_bactid, suffix = c("_tempmicroorganisms", ""))
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# antibiotic classes
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aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
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tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart
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polymyxins <- c(poly, coli)
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macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clinda is set apart
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glycopeptides <- c(vanc, teic)
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streptogramins <- c(qida, pris) # should officially also be quinupristin/dalfopristin
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cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
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carbapenems <- c(erta, imip, mero)
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aminopenicillins <- c(ampi, amox)
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ureidopenicillins <- c(pita, azlo, mezl)
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fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
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if (info == TRUE) {
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cat(
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paste0(
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'\nApplying rules to ',
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tbl[!is.na(tbl$genus),] %>% nrow() %>% format(big.mark = ","),
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' rows according to "EUCAST Expert Rules Version ', EUCAST_VERSION, '"\n')
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)
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}
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# Table 1: Intrinsic resistance in Enterobacteriaceae ----
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if (info == TRUE) {
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cat('- Table 1: Intrinsic resistance in Enterobacteriaceae\n')
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}
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# Intrisiek R for this group
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edit_rsi(to = 'R',
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rows = which(tbl$family == 'Enterobacteriaceae'),
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cols = c(peni, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
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# Citrobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
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cols = c(aminopenicillins, tica))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
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cols = c(aminopenicillins, amcl, czol, cfox))
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# Enterobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
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cols = c(aminopenicillins, amcl, czol, cfox))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
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cols = c(aminopenicillins, amcl, czol, cfox))
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# Escherichia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Escherichia hermanni'),
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cols = c(aminopenicillins, tica))
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# Hafnia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Hafnia alvei'),
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cols = c(aminopenicillins, amcl, czol, cfox))
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# Klebsiella
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Klebsiella'),
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cols = c(aminopenicillins, tica))
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# Morganella / Proteus
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Morganella morganii'),
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cols = c(aminopenicillins, amcl, czol, tetracyclines, polymyxins, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus mirabilis'),
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cols = c(tetracyclines, tige, polymyxins, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus penneri'),
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cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus vulgaris'),
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cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
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# Providencia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Providencia rettgeri'),
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cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Providencia stuartii'),
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cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
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# Raoultella
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Raoultella'),
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cols = c(aminopenicillins, tica))
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# Serratia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Serratia marcescens'),
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cols = c(aminopenicillins, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxins, nitr))
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# Yersinia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
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cols = c(aminopenicillins, amcl, tica, czol, cfox))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
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cols = c(poly, coli))
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# Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria ----
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if (info == TRUE) {
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cat('- Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria\n')
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}
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# Intrisiek R for this group
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edit_rsi(to = 'R',
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rows = which(tbl$genus %in% c('Achromobacter',
|
|
'Acinetobacter',
|
|
'Alcaligenes',
|
|
'Bordatella',
|
|
'Burkholderia',
|
|
'Elizabethkingia',
|
|
'Flavobacterium',
|
|
'Ochrobactrum',
|
|
'Pseudomonas',
|
|
'Stenotrophomonas')),
|
|
cols = c(peni, cfox, cfur, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
|
|
# Acinetobacter
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
|
|
cols = c(aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
|
|
# Achromobacter
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
|
|
cols = c(aminopenicillins, czol, cfot, cftr, erta))
|
|
# Burkholderia
|
|
edit_rsi(to = 'R',
|
|
# onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
|
|
rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
|
|
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins))
|
|
# Elizabethkingia
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
|
|
cols = c(aminopenicillins, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxins))
|
|
# Ochrobactrum
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
|
|
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
|
|
# Pseudomonas
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
|
|
cols = c(aminopenicillins, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
|
|
# Stenotrophomonas
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
|
|
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr))
|
|
|
|
|
|
# Table 3: Intrinsic resistance in other Gram-negative bacteria ----
|
|
if (info == TRUE) {
|
|
cat('- Table 3: Intrinsic resistance in other Gram-negative bacteria\n')
|
|
}
|
|
# Intrisiek R for this group
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus %in% c('Haemophilus',
|
|
'Moraxella',
|
|
'Neisseria',
|
|
'Campylobacter')),
|
|
cols = c(glycopeptides, linc, dapt, line))
|
|
# Haemophilus
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Haemophilus influenzae'),
|
|
cols = c(fusi, streptogramins))
|
|
# Moraxella
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Moraxella catarrhalis'),
|
|
cols = trim)
|
|
# Neisseria
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Neisseria'),
|
|
cols = trim)
|
|
# Campylobacter
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Campylobacter fetus'),
|
|
cols = c(fusi, streptogramins, trim, nali))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Campylobacter (jejuni|coli)'),
|
|
cols = c(fusi, streptogramins, trim))
|
|
|
|
|
|
# Table 4: Intrinsic resistance in Gram-positive bacteria ----
|
|
if (info == TRUE) {
|
|
cat('- Table 4: Intrinsic resistance in Gram-positive bacteria\n')
|
|
}
|
|
# Intrisiek R for this group
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$gramstain %like% 'Positi(e|)(v|f)'),
|
|
cols = c(aztr, polymyxins, nali))
|
|
# Staphylococcus
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Staphylococcus saprophyticus'),
|
|
cols = c(fusi, cfta, fosf, novo))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Staphylococcus (cohnii|xylosus)'),
|
|
cols = c(cfta, novo))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Staphylococcus capitis'),
|
|
cols = c(cfta, fosf))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
|
|
cols = cfta)
|
|
# Streptococcus
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Streptococcus'),
|
|
cols = c(fusi, cfta, aminoglycosides))
|
|
# Enterococcus
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Enterococcus faecalis'),
|
|
cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, clin, qida, trim, trsu))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Enterococcus (gallinarum|casseliflavus)'),
|
|
cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, clin, qida, vanc, trim, trsu))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Enterococcus faecium'),
|
|
cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, trim, trsu))
|
|
# Corynebacterium
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Corynebacterium'),
|
|
cols = fosf)
|
|
# Listeria
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Listeria monocytogenes'),
|
|
cols = c(cfta, cephalosporins[cephalosporins != cfta]))
|
|
# overig
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus %in% c('Leuconostoc', 'Pediococcus')),
|
|
cols = c(vanc, teic))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Lactobacillus'),
|
|
cols = c(vanc, teic))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Clostridium (ramosum|innocuum)'),
|
|
cols = vanc)
|
|
|
|
# Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci ----
|
|
if (info == TRUE) {
|
|
cat('- Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci\n')
|
|
}
|
|
# rule 8.3
|
|
if (!is.na(peni)) {
|
|
edit_rsi(to = 'S',
|
|
rows = which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|dysgalactiae|groep A|groep B|groep C|groep G)'
|
|
& tbl[, peni] == 'S'),
|
|
cols = c(aminopenicillins, cephalosporins, carbapenems))
|
|
}
|
|
# rule 8.6
|
|
if (!is.na(ampi)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Enterococcus'
|
|
& tbl[, ampi] == 'R'),
|
|
cols = c(ureidopenicillins, carbapenems))
|
|
}
|
|
if (!is.na(amox)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Enterococcus'
|
|
& tbl[, amox] == 'R'),
|
|
cols = c(ureidopenicillins, carbapenems))
|
|
}
|
|
|
|
# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
|
|
if (info == TRUE) {
|
|
cat('- Table 9: Interpretive rules for B-lactam agents and Gram-negative rods\n')
|
|
}
|
|
# rule 9.3
|
|
if (!is.na(tica) & !is.na(pita)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, tica] == 'R'
|
|
& tbl[, pita] == 'S'),
|
|
cols = pita)
|
|
}
|
|
|
|
# Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria ----
|
|
if (info == TRUE) {
|
|
cat('- Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria\n')
|
|
}
|
|
# rule 10.2
|
|
if (!is.na(ampi)) {
|
|
# you should know first if the are B-lactamase positive, so do not run for now
|
|
# edit_rsi(to = 'R',
|
|
# rows = which(tbl$fullname %like% '^Haemophilus influenza'
|
|
# & tbl[, ampi] == 'R'),
|
|
# cols = c(ampi, amox, amcl, pita, cfur))
|
|
}
|
|
|
|
# Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins ----
|
|
if (info == TRUE) {
|
|
cat('- Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins\n')
|
|
}
|
|
# rule 11.1
|
|
if (!is.na(eryt)) {
|
|
if (!is.na(azit)) {
|
|
tbl[, azit] <- tbl[, eryt]
|
|
}
|
|
if (!is.na(clar)) {
|
|
tbl[, clar] <- tbl[, eryt]
|
|
}
|
|
}
|
|
|
|
# Table 12: Interpretive rules for aminoglycosides ----
|
|
if (info == TRUE) {
|
|
cat('- Table 12: Interpretive rules for aminoglycosides\n')
|
|
}
|
|
# rule 12.2
|
|
if (!is.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, tobr] == 'R'),
|
|
cols = c(kana, amik))
|
|
}
|
|
# rule 12.3
|
|
if (!is.na(gent)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, gent] == 'R'),
|
|
cols = aminoglycosides)
|
|
}
|
|
# rule 12.8
|
|
if (!is.na(gent) & !is.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, gent] == 'I'
|
|
& tbl[, tobr] == 'S'),
|
|
cols = gent)
|
|
}
|
|
# rule 12.9
|
|
if (!is.na(gent) & !is.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, tobr] == 'I'
|
|
& tbl[, gent] == 'R'),
|
|
cols = tobr)
|
|
}
|
|
|
|
|
|
# Table 13: Interpretive rules for quinolones ----
|
|
if (info == TRUE) {
|
|
cat('- Table 13: Interpretive rules for quinolones\n')
|
|
}
|
|
# rule 13.2
|
|
if (!is.na(moxi)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, moxi] == 'R'),
|
|
cols = fluoroquinolones)
|
|
}
|
|
# rule 13.4
|
|
if (!is.na(moxi)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Streptococcus pneumoniae'
|
|
& tbl[, moxi] == 'R'),
|
|
cols = fluoroquinolones)
|
|
}
|
|
# rule 13.5
|
|
if (!is.na(cipr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, cipr] == 'R'),
|
|
cols = fluoroquinolones)
|
|
}
|
|
# rule 13.8
|
|
if (!is.na(cipr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Neisseria gonorrhoeae'
|
|
& tbl[, cipr] == 'R'),
|
|
cols = fluoroquinolones)
|
|
}
|
|
|
|
|
|
# Other ----
|
|
if (info == TRUE) {
|
|
cat('- Non-EUCAST: trim = R where trsu = R and ampi = R where amcl = R\n')
|
|
}
|
|
if (!is.na(amcl)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl[, amcl] == 'R'),
|
|
cols = ampi)
|
|
}
|
|
if (!is.na(trsu)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl[, trsu] == 'R'),
|
|
cols = trim)
|
|
}
|
|
if (info == TRUE) {
|
|
cat('- Non-EUCAST: trsu = S where trim = S and amcl = S where ampi = S\n')
|
|
}
|
|
if (!is.na(amcl)) {
|
|
edit_rsi(to = 'S',
|
|
rows = which(tbl[, ampi] == 'S'),
|
|
cols = amcl)
|
|
}
|
|
if (!is.na(trsu)) {
|
|
edit_rsi(to = 'S',
|
|
rows = which(tbl[, trim] == 'S'),
|
|
cols = trsu)
|
|
}
|
|
# amox = ampi
|
|
if (!is.na(ampi) & !is.na(amox)) {
|
|
tbl[, amox] <- tbl %>% pull(ampi)
|
|
}
|
|
|
|
# Remove added columns again
|
|
microorganisms.ncol <- ncol(AMR::microorganisms) - 2
|
|
tbl.ncol <- ncol(tbl)
|
|
tbl <- tbl %>% select(-c((tbl.ncol - microorganisms.ncol):tbl.ncol))
|
|
# and remove added suffices
|
|
colnames(tbl) <- gsub("_tempmicroorganisms", "", colnames(tbl))
|
|
|
|
if (info == TRUE) {
|
|
cat('Done.\n\nEUCAST Expert rules applied to',
|
|
total_rows %>% unique() %>% length() %>% format(big.mark = ","),
|
|
'different rows; overwritten a total of',
|
|
total %>% format(big.mark = ","), 'test results.\n\n')
|
|
}
|
|
|
|
tbl
|
|
}
|
|
|
|
#' @rdname EUCAST
|
|
#' @export
|
|
interpretive_reading <- function(...) {
|
|
EUCAST_rules(...)
|
|
}
|
|
|
|
#' Poperties of a microorganism
|
|
#'
|
|
#' @param bactid ID of a microorganisme, like \code{"STAAUR} and \code{"ESCCOL}
|
|
#' @param property One of the values \code{bactid}, \code{bactsys}, \code{family}, \code{genus}, \code{species}, \code{subspecies}, \code{fullname}, \code{type}, \code{gramstain}, \code{aerobic}
|
|
#' @export
|
|
#' @importFrom dplyr %>% filter select
|
|
#' @seealso \code{\link{microorganisms}}
|
|
mo_property <- function(bactid, property = 'fullname') {
|
|
|
|
mocode <- as.character(bactid)
|
|
|
|
for (i in 1:length(mocode)) {
|
|
bug <- mocode[i]
|
|
|
|
if (!is.na(bug)) {
|
|
result = tryCatch({
|
|
mocode[i] <-
|
|
AMR::microorganisms %>%
|
|
filter(bactid == bug) %>%
|
|
select(property) %>%
|
|
unlist() %>%
|
|
as.character()
|
|
}, error = function(error_condition) {
|
|
warning('Code ', bug, ' not found in bacteria list.')
|
|
}, finally = {
|
|
if (mocode[i] == bug & !property %in% c('bactid', 'bactsys')) {
|
|
mocode[i] <- NA
|
|
}
|
|
})
|
|
}
|
|
|
|
}
|
|
mocode
|
|
}
|