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AMR/R/eucast.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' EUCAST expert rules
#'
#' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
#' @param col_mo column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}
#' @param info print progress
#' @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 name of an antibiotic. 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.
#' @param col_bactid Deprecated. Use \code{col_mo} instead.
#' @param ... parameters that are passed on to \code{EUCAST_rules}
#' @section Antibiotics:
#' Abbrevations of the column containing antibiotics:
#'
#' \strong{amcl}: amoxicillin and beta-lactamase inhibitor (\emph{J01CR02}),
#' \strong{amik}: amikacin (\emph{J01GB06}),
#' \strong{amox}: amoxicillin (\emph{J01CA04}),
#' \strong{ampi}: ampicillin (\emph{J01CA01}),
#' \strong{azit}: azithromycin (\emph{J01FA10}),
#' \strong{azlo}: azlocillin (\emph{J01CA09}),
#' \strong{aztr}: aztreonam (\emph{J01DF01}),
#' \strong{cefa}: cefaloridine (\emph{J01DB02}),
#' \strong{cfep}: cefepime (\emph{J01DE01}),
#' \strong{cfot}: cefotaxime (\emph{J01DD01}),
#' \strong{cfox}: cefoxitin (\emph{J01DC01}),
#' \strong{cfra}: cefradine (\emph{J01DB09}),
#' \strong{cfta}: ceftazidime (\emph{J01DD02}),
#' \strong{cftr}: ceftriaxone (\emph{J01DD04}),
#' \strong{cfur}: cefuroxime (\emph{J01DC02}),
#' \strong{chlo}: chloramphenicol (\emph{J01BA01}),
#' \strong{cipr}: ciprofloxacin (\emph{J01MA02}),
#' \strong{clar}: clarithromycin (\emph{J01FA09}),
#' \strong{clin}: clindamycin (\emph{J01FF01}),
#' \strong{clox}: flucloxacillin (\emph{J01CF05}),
#' \strong{coli}: colistin (\emph{J01XB01}),
#' \strong{czol}: cefazolin (\emph{J01DB04}),
#' \strong{dapt}: daptomycin (\emph{J01XX09}),
#' \strong{doxy}: doxycycline (\emph{J01AA02}),
#' \strong{erta}: ertapenem (\emph{J01DH03}),
#' \strong{eryt}: erythromycin (\emph{J01FA01}),
#' \strong{fosf}: fosfomycin (\emph{J01XX01}),
#' \strong{fusi}: fusidic acid (\emph{J01XC01}),
#' \strong{gent}: gentamicin (\emph{J01GB03}),
#' \strong{imip}: imipenem and cilastatin (\emph{J01DH51}),
#' \strong{kana}: kanamycin (\emph{J01GB04}),
#' \strong{levo}: levofloxacin (\emph{J01MA12}),
#' \strong{linc}: lincomycin (\emph{J01FF02}),
#' \strong{line}: linezolid (\emph{J01XX08}),
#' \strong{mero}: meropenem (\emph{J01DH02}),
#' \strong{mezl}: mezlocillin (\emph{J01CA10}),
#' \strong{mino}: minocycline (\emph{J01AA08}),
#' \strong{moxi}: moxifloxacin (\emph{J01MA14}),
#' \strong{nali}: nalidixic acid (\emph{J01MB02}),
#' \strong{neom}: neomycin (\emph{J01GB05}),
#' \strong{neti}: netilmicin (\emph{J01GB07}),
#' \strong{nitr}: nitrofurantoin (\emph{J01XE01}),
#' \strong{norf}: norfloxacin (\emph{J01MA06}),
#' \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
#' \strong{oflo}: ofloxacin (\emph{J01MA01}),
#' \strong{peni}: penicillins, combinations with other antibacterials (\emph{J01RA01}),
#' \strong{pita}: piperacillin and beta-lactamase inhibitor (\emph{J01CR05}),
#' \strong{poly}: polymyxin B (\emph{J01XB02}),
#' \strong{pris}: pristinamycin (\emph{J01FG01}),
#' \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
#' \strong{rifa}: rifampicin (\emph{J04AB02}),
#' \strong{roxi}: roxithromycin (\emph{J01FA06}),
#' \strong{siso}: sisomicin (\emph{J01GB08}),
#' \strong{teic}: teicoplanin (\emph{J01XA02}),
#' \strong{tetr}: tetracycline (\emph{J01AA07}),
#' \strong{tica}: ticarcillin (\emph{J01CA13}),
#' \strong{tige}: tigecycline (\emph{J01AA12}),
#' \strong{tobr}: tobramycin (\emph{J01GB01}),
#' \strong{trim}: trimethoprim (\emph{J01EA01}),
#' \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
#' \strong{vanc}: vancomycin (\emph{J01XA01}).
#' @keywords interpretive eucast reading resistance
#' @rdname EUCAST
#' @export
#' @importFrom dplyr %>% left_join select
#' @return table with edited variables of antibiotics.
#' @source
#' EUCAST Expert Rules Version 2.0: \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} \cr
#' \cr
#' EUCAST Expert Rules Version 3.1 (Intrinsic Resistance and Exceptional Phenotypes Tables): \cr
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
#' @examples
#' a <- EUCAST_rules(septic_patients)
#' a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
#' "ENCFAE", # Enterococcus faecalis
#' "ESCCOL", # Escherichia coli
#' "KLEPNE", # Klebsiella pneumoniae
#' "PSEAER"), # Pseudomonas aeruginosa
#' vanc = "-", # Vancomycin
#' amox = "-", # Amoxicillin
#' coli = "-", # Colistin
#' cfta = "-", # Ceftazidime
#' cfur = "-", # Cefuroxime
#' stringsAsFactors = FALSE)
#' a
#'
#' b <- EUCAST_rules(a)
#' b
EUCAST_rules <- function(tbl,
col_mo = 'mo',
info = TRUE,
amcl = 'amcl',
amik = 'amik',
amox = 'amox',
ampi = 'ampi',
azit = 'azit',
azlo = 'azlo',
aztr = 'aztr',
cefa = 'cefa',
cfep = 'cfep',
cfot = 'cfot',
cfox = 'cfox',
cfra = 'cfra',
cfta = 'cfta',
cftr = 'cftr',
cfur = 'cfur',
chlo = 'chlo',
cipr = 'cipr',
clar = 'clar',
clin = 'clin',
clox = 'clox',
coli = 'coli',
czol = 'czol',
dapt = 'dapt',
doxy = 'doxy',
erta = 'erta',
eryt = 'eryt',
fosf = 'fosf',
fusi = 'fusi',
gent = 'gent',
imip = 'imip',
kana = 'kana',
levo = 'levo',
linc = 'linc',
line = 'line',
mero = 'mero',
mezl = 'mezl',
mino = 'mino',
moxi = 'moxi',
nali = 'nali',
neom = 'neom',
neti = 'neti',
nitr = 'nitr',
norf = 'norf',
novo = 'novo',
oflo = 'oflo',
peni = 'peni',
pita = 'pita',
poly = 'poly',
pris = 'pris',
qida = 'qida',
rifa = 'rifa',
roxi = 'roxi',
siso = 'siso',
teic = 'teic',
tetr = 'tetr',
tica = 'tica',
tige = 'tige',
tobr = 'tobr',
trim = 'trim',
trsu = 'trsu',
vanc = 'vanc',
col_bactid = 'bactid') {
EUCAST_VERSION <- "3.1"
if (col_bactid %in% colnames(tbl)) {
col_mo <- col_bactid
warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
}
if (!col_mo %in% colnames(tbl)) {
stop('Column ', col_mo, ' not found.', call. = FALSE)
}
# check columns
col.list <- c(amcl, amik, amox, ampi, azit, azlo, 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, mezl, mino, moxi, nali, neom, neti, nitr,
novo, norf, oflo, peni, pita, poly, pris, qida, rifa, roxi, siso,
teic, tetr, tica, tige, tobr, trim, trsu, vanc)
col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
amcl <- col.list[amcl]
amik <- col.list[amik]
amox <- col.list[amox]
ampi <- col.list[ampi]
azit <- col.list[azit]
azlo <- col.list[azlo]
aztr <- col.list[aztr]
cefa <- col.list[cefa]
cfep <- col.list[cfep]
cfot <- col.list[cfot]
cfox <- col.list[cfox]
cfra <- col.list[cfra]
cfta <- col.list[cfta]
cftr <- col.list[cftr]
cfur <- col.list[cfur]
chlo <- col.list[chlo]
cipr <- col.list[cipr]
clar <- col.list[clar]
clin <- col.list[clin]
clox <- col.list[clox]
coli <- col.list[coli]
czol <- col.list[czol]
dapt <- col.list[dapt]
doxy <- col.list[doxy]
erta <- col.list[erta]
eryt <- col.list[eryt]
fosf <- col.list[fosf]
fusi <- col.list[fusi]
gent <- col.list[gent]
imip <- col.list[imip]
kana <- col.list[kana]
levo <- col.list[levo]
linc <- col.list[linc]
line <- col.list[line]
mero <- col.list[mero]
mezl <- col.list[mezl]
mino <- col.list[mino]
moxi <- col.list[moxi]
nali <- col.list[nali]
neom <- col.list[neom]
neti <- col.list[neti]
nitr <- col.list[nitr]
norf <- col.list[norf]
novo <- col.list[novo]
oflo <- col.list[oflo]
peni <- col.list[peni]
pita <- col.list[pita]
poly <- col.list[poly]
pris <- col.list[pris]
qida <- col.list[qida]
rifa <- col.list[rifa]
roxi <- col.list[roxi]
siso <- col.list[siso]
teic <- col.list[teic]
tetr <- col.list[tetr]
tica <- col.list[tica]
tige <- col.list[tige]
tobr <- col.list[tobr]
trim <- col.list[trim]
trsu <- col.list[trsu]
vanc <- col.list[vanc]
total <- 0
total_rows <- integer(0)
# helper function for editing the table
edit_rsi <- function(to, rows, cols, EUCAST_rule = "") {
# later: use this as attribute for the edited observations
EUCAST_rule <- trimws(paste("EUCAST rule", EUCAST_rule))
cols <- cols[!is.na(cols)]
if (length(rows) > 0 & length(cols) > 0) {
tbl[rows, cols] <<- to
total <<- total + (length(rows) * length(cols))
total_rows <<- c(total_rows, rows)
}
}
# join to microorganisms data set
col_mo_original <- NULL
if (!tbl %>% pull(col_mo) %>% is.mo()) {
col_mo_original <- tbl %>% pull(col_mo)
tbl[, col_mo] <- as.mo(tbl[, col_mo])
}
tbl <- tbl %>% left_join_microorganisms(by = col_mo, suffix = c("_tempmicroorganisms", ""))
# antibiotic classes
aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart
polymyxins <- c(poly, coli)
macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clinda is set apart
glycopeptides <- c(vanc, teic)
streptogramins <- c(qida, pris) # should officially also be quinupristin/dalfopristin
cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
carbapenems <- c(erta, imip, mero)
aminopenicillins <- c(ampi, amox)
ureidopenicillins <- c(pita, azlo, mezl)
fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
if (info == TRUE) {
cat(
paste0(
'\nApplying rules to ',
tbl[!is.na(tbl$genus),] %>% nrow() %>% format(big.mark = ","),
' rows according to "EUCAST Expert Rules Version ', EUCAST_VERSION, '"\n')
)
}
# Table 1: Intrinsic resistance in Enterobacteriaceae ----
if (info == TRUE) {
cat('- Table 1: Intrinsic resistance in Enterobacteriaceae\n')
}
# Intrisiek R for this group
edit_rsi(to = 'R',
rows = which(tbl$family == 'Enterobacteriaceae'),
cols = c(peni, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
# Citrobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
cols = c(aminopenicillins, tica))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Enterobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
cols = c(aminopenicillins, amcl, czol, cfox))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Escherichia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Escherichia hermanni'),
cols = c(aminopenicillins, tica))
# Hafnia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Hafnia alvei'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Klebsiella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Klebsiella'),
cols = c(aminopenicillins, tica))
# Morganella / Proteus
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Morganella morganii'),
cols = c(aminopenicillins, amcl, czol, tetracyclines, polymyxins, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus mirabilis'),
cols = c(tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus penneri'),
cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus vulgaris'),
cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
# Providencia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Providencia rettgeri'),
cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Providencia stuartii'),
cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
# Raoultella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Raoultella'),
cols = c(aminopenicillins, tica))
# Serratia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Serratia marcescens'),
cols = c(aminopenicillins, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxins, nitr))
# Yersinia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
cols = c(aminopenicillins, amcl, tica, czol, cfox))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
cols = c(poly, coli))
# Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria ----
if (info == TRUE) {
cat('- Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria\n')
}
# Intrisiek R for this group
edit_rsi(to = 'R',
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))
# restore old col_mo values if needed
if (!is.null(col_mo_original)) {
tbl[, col_mo] <- col_mo_original
}
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(...)
}
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