mirror of https://github.com/msberends/AMR.git
727 lines
29 KiB
R
727 lines
29 KiB
R
# ==================================================================== #
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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,aztr,cefa,cfra,cfep,cfot,cfox,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mino,moxi,nali,neom,neti,nitr,novo,norf,oflo,peni,pita,poly,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 column will be skipped.
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#' @param ... parameters that are passed on to \code{EUCAST_rules}
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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 <- 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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aztr = 'aztr',
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cefa = 'cefa',
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cfra = 'cfra',
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cfep = 'cfep',
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cfot = 'cfot',
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cfox = 'cfox',
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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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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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novo = 'novo',
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norf = 'norf',
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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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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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# support using columns as objects; the tidyverse way
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amcl <- quasiquotate(deparse(substitute(amcl)), amcl)
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amik <- quasiquotate(deparse(substitute(amik)), amik)
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amox <- quasiquotate(deparse(substitute(amox)), amox)
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ampi <- quasiquotate(deparse(substitute(ampi)), ampi)
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azit <- quasiquotate(deparse(substitute(azit)), azit)
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aztr <- quasiquotate(deparse(substitute(aztr)), aztr)
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cefa <- quasiquotate(deparse(substitute(cefa)), cefa)
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cfra <- quasiquotate(deparse(substitute(cfra)), cfra)
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cfep <- quasiquotate(deparse(substitute(cfep)), cfep)
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cfot <- quasiquotate(deparse(substitute(cfot)), cfot)
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cfox <- quasiquotate(deparse(substitute(cfox)), cfox)
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cfta <- quasiquotate(deparse(substitute(cfta)), cfta)
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cftr <- quasiquotate(deparse(substitute(cftr)), cftr)
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cfur <- quasiquotate(deparse(substitute(cfur)), cfur)
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chlo <- quasiquotate(deparse(substitute(chlo)), chlo)
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cipr <- quasiquotate(deparse(substitute(cipr)), cipr)
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clar <- quasiquotate(deparse(substitute(clar)), clar)
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clin <- quasiquotate(deparse(substitute(clin)), clin)
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clox <- quasiquotate(deparse(substitute(clox)), clox)
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coli <- quasiquotate(deparse(substitute(coli)), coli)
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czol <- quasiquotate(deparse(substitute(czol)), czol)
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dapt <- quasiquotate(deparse(substitute(dapt)), dapt)
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doxy <- quasiquotate(deparse(substitute(doxy)), doxy)
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erta <- quasiquotate(deparse(substitute(erta)), erta)
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eryt <- quasiquotate(deparse(substitute(eryt)), eryt)
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fosf <- quasiquotate(deparse(substitute(fosf)), fosf)
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fusi <- quasiquotate(deparse(substitute(fusi)), fusi)
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gent <- quasiquotate(deparse(substitute(gent)), gent)
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imip <- quasiquotate(deparse(substitute(imip)), imip)
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kana <- quasiquotate(deparse(substitute(kana)), kana)
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levo <- quasiquotate(deparse(substitute(levo)), levo)
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linc <- quasiquotate(deparse(substitute(linc)), linc)
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line <- quasiquotate(deparse(substitute(line)), line)
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mero <- quasiquotate(deparse(substitute(mero)), mero)
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mino <- quasiquotate(deparse(substitute(mino)), mino)
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moxi <- quasiquotate(deparse(substitute(moxi)), moxi)
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nali <- quasiquotate(deparse(substitute(nali)), nali)
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neom <- quasiquotate(deparse(substitute(neom)), neom)
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neti <- quasiquotate(deparse(substitute(neti)), neti)
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nitr <- quasiquotate(deparse(substitute(nitr)), nitr)
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novo <- quasiquotate(deparse(substitute(novo)), novo)
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norf <- quasiquotate(deparse(substitute(norf)), norf)
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oflo <- quasiquotate(deparse(substitute(oflo)), oflo)
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peni <- quasiquotate(deparse(substitute(peni)), peni)
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pita <- quasiquotate(deparse(substitute(pita)), pita)
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poly <- quasiquotate(deparse(substitute(poly)), poly)
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qida <- quasiquotate(deparse(substitute(qida)), qida)
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rifa <- quasiquotate(deparse(substitute(rifa)), rifa)
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roxi <- quasiquotate(deparse(substitute(roxi)), roxi)
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siso <- quasiquotate(deparse(substitute(siso)), siso)
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teic <- quasiquotate(deparse(substitute(teic)), teic)
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tetr <- quasiquotate(deparse(substitute(tetr)), tetr)
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tica <- quasiquotate(deparse(substitute(tica)), tica)
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tige <- quasiquotate(deparse(substitute(tige)), tige)
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tobr <- quasiquotate(deparse(substitute(tobr)), tobr)
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trim <- quasiquotate(deparse(substitute(trim)), trim)
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trsu <- quasiquotate(deparse(substitute(trsu)), trsu)
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vanc <- quasiquotate(deparse(substitute(vanc)), vanc)
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if (!col_bactid %in% colnames(tbl)) {
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stop('Column ', col_bactid, ' not found.')
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}
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# check columns
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col.list <- c(amcl, amik, amox, ampi, azit, 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, mino, moxi, nali, neom, neti, nitr,
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novo, norf, oflo, peni, pita, poly, qida, rifa, roxi, siso,
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teic, tetr, tica, tige, tobr, trim, trsu, vanc)
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col.list <- col.list[!is.na(col.list)]
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col.list.bak <- col.list
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# are they available as upper case or lower case then?
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for (i in 1:length(col.list)) {
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if (toupper(col.list[i]) %in% colnames(tbl)) {
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col.list[i] <- toupper(col.list[i])
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} else if (tolower(col.list[i]) %in% colnames(tbl)) {
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col.list[i] <- tolower(col.list[i])
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} else if (!col.list[i] %in% colnames(tbl)) {
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col.list[i] <- NA
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}
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}
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if (!all(col.list %in% colnames(tbl))) {
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if (info == TRUE) {
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cat('\n')
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}
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if (info == TRUE) {
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warning('These columns do not exist and will be ignored: ',
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col.list.bak[!(col.list %in% colnames(tbl))] %>% toString(),
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immediate. = TRUE,
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call. = FALSE)
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}
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}
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amcl <- col.list[1]
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amik <- col.list[2]
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amox <- col.list[3]
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ampi <- col.list[4]
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azit <- col.list[5]
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aztr <- col.list[6]
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cefa <- col.list[7]
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cfra <- col.list[8]
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cfep <- col.list[9]
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cfot <- col.list[10]
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cfox <- col.list[11]
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cfta <- col.list[12]
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cftr <- col.list[13]
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cfur <- col.list[14]
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chlo <- col.list[15]
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cipr <- col.list[16]
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clar <- col.list[17]
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clin <- col.list[18]
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clox <- col.list[19]
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coli <- col.list[20]
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czol <- col.list[21]
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dapt <- col.list[22]
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doxy <- col.list[23]
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erta <- col.list[24]
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eryt <- col.list[25]
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fosf <- col.list[26]
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fusi <- col.list[27]
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gent <- col.list[28]
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imip <- col.list[29]
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kana <- col.list[30]
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levo <- col.list[31]
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linc <- col.list[32]
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line <- col.list[33]
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mero <- col.list[34]
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mino <- col.list[35]
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moxi <- col.list[36]
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nali <- col.list[37]
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neom <- col.list[38]
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neti <- col.list[39]
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nitr <- col.list[40]
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novo <- col.list[41]
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norf <- col.list[42]
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oflo <- col.list[43]
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peni <- col.list[44]
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pita <- col.list[45]
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poly <- col.list[46]
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qida <- col.list[47]
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rifa <- col.list[48]
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roxi <- col.list[49]
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siso <- col.list[50]
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teic <- col.list[51]
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tetr <- col.list[52]
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tica <- col.list[53]
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tige <- col.list[54]
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tobr <- col.list[55]
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trim <- col.list[56]
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trsu <- col.list[57]
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vanc <- col.list[58]
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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) {
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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 table
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joinby <- colnames(AMR::microorganisms)[1]
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names(joinby) <- col_bactid
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tbl <- tbl %>% left_join(y = AMR::microorganisms, by = joinby, 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 <- qida # should officially also be pristinamycin and 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 <- pita # should officially also be azlo and mezlo
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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$genus %in% c('Achromobacter',
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|
'Acinetobacter',
|
|
'Alcaligenes',
|
|
'Bordatella',
|
|
'Burkholderia',
|
|
'Elizabethkingia',
|
|
'Flavobacterium',
|
|
'Ochrobactrum',
|
|
'Pseudomonas',
|
|
'Stenotrophomonas')),
|
|
cols = c(peni, cfox, cfur, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
|
|
# Acinetobacter
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$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 (!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 (isolates); edited 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
|
|
}
|