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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 rules
#'
#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
#' @param info print progress
#' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}
#' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected
#' @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,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Details
#' @param col_bactid deprecated, use \code{col_mo} instead.
#' @param ... parameters that are passed on to \code{EUCAST_rules}
#' @inheritParams first_isolate
#' @details To define antibiotics column names, input a text or use \code{NA} to skip a column (e.g. \code{tica = NA}). Non-existing columns will anyway be skipped with a warning. See the Antibiotics section for an explanation of the abbreviations.
#' @section Antibiotics:
#' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
#'
#' \strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}),
#' \strong{amik}: amikacin (\emph{J01GB06}),
#' \strong{amox}: amoxicillin (\emph{J01CA04}),
#' \strong{ampi}: ampicillin (\emph{J01CA01}),
#' \strong{azit}: azithromycin (\emph{J01FA10}),
#' \strong{azlo}: azlocillin (\emph{J01CA09}),
#' \strong{aztr}: aztreonam (\emph{J01DF01}),
#' \strong{cefa}: cefaloridine (\emph{J01DB02}),
#' \strong{cfep}: cefepime (\emph{J01DE01}),
#' \strong{cfot}: cefotaxime (\emph{J01DD01}),
#' \strong{cfox}: cefoxitin (\emph{J01DC01}),
#' \strong{cfra}: cefradine (\emph{J01DB09}),
#' \strong{cfta}: ceftazidime (\emph{J01DD02}),
#' \strong{cftr}: ceftriaxone (\emph{J01DD04}),
#' \strong{cfur}: cefuroxime (\emph{J01DC02}),
#' \strong{chlo}: chloramphenicol (\emph{J01BA01}),
#' \strong{cipr}: ciprofloxacin (\emph{J01MA02}),
#' \strong{clar}: clarithromycin (\emph{J01FA09}),
#' \strong{clin}: clindamycin (\emph{J01FF01}),
#' \strong{clox}: flucloxacillin (\emph{J01CF05}),
#' \strong{coli}: colistin (\emph{J01XB01}),
#' \strong{czol}: cefazolin (\emph{J01DB04}),
#' \strong{dapt}: daptomycin (\emph{J01XX09}),
#' \strong{doxy}: doxycycline (\emph{J01AA02}),
#' \strong{erta}: ertapenem (\emph{J01DH03}),
#' \strong{eryt}: erythromycin (\emph{J01FA01}),
#' \strong{fosf}: fosfomycin (\emph{J01XX01}),
#' \strong{fusi}: fusidic acid (\emph{J01XC01}),
#' \strong{gent}: gentamicin (\emph{J01GB03}),
#' \strong{imip}: imipenem (\emph{J01DH51}),
#' \strong{kana}: kanamycin (\emph{J01GB04}),
#' \strong{levo}: levofloxacin (\emph{J01MA12}),
#' \strong{linc}: lincomycin (\emph{J01FF02}),
#' \strong{line}: linezolid (\emph{J01XX08}),
#' \strong{mero}: meropenem (\emph{J01DH02}),
#' \strong{mezl}: mezlocillin (\emph{J01CA10}),
#' \strong{mino}: minocycline (\emph{J01AA08}),
#' \strong{moxi}: moxifloxacin (\emph{J01MA14}),
#' \strong{nali}: nalidixic acid (\emph{J01MB02}),
#' \strong{neom}: neomycin (\emph{J01GB05}),
#' \strong{neti}: netilmicin (\emph{J01GB07}),
#' \strong{nitr}: nitrofurantoin (\emph{J01XE01}),
#' \strong{norf}: norfloxacin (\emph{J01MA06}),
#' \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
#' \strong{oflo}: ofloxacin (\emph{J01MA01}),
#' \strong{peni}: penicillin (\emph{J01RA01}),
#' \strong{pipe}: piperacillin (\emph{J01CA12}),
#' \strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
#' \strong{poly}: polymyxin B (\emph{J01XB02}),
#' \strong{pris}: pristinamycin (\emph{J01FG01}),
#' \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
#' \strong{rifa}: rifampicin (\emph{J04AB02}),
#' \strong{roxi}: roxithromycin (\emph{J01FA06}),
#' \strong{siso}: sisomicin (\emph{J01GB08}),
#' \strong{teic}: teicoplanin (\emph{J01XA02}),
#' \strong{tetr}: tetracycline (\emph{J01AA07}),
#' \strong{tica}: ticarcillin (\emph{J01CA13}),
#' \strong{tige}: tigecycline (\emph{J01AA12}),
#' \strong{tobr}: tobramycin (\emph{J01GB01}),
#' \strong{trim}: trimethoprim (\emph{J01EA01}),
#' \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
#' \strong{vanc}: vancomycin (\emph{J01XA01}).
#' @keywords interpretive eucast reading resistance
#' @rdname EUCAST
#' @export
#' @importFrom dplyr %>% select pull mutate_at vars
#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic
#' @return The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info.
#' @source
#' \itemize{
#' \item{
#' EUCAST Expert Rules. Version 2.0, 2012. \cr
#' Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
#' \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
#' }
#' \item{
#' EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
#' }
#' \item{
#' EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. \cr
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx}
#' }
#' }
#' @examples
#' a <- EUCAST_rules(septic_patients)
#'
#' a <- data.frame(mo = c("Staphylococcus aureus",
#' "Enterococcus faecalis",
#' "Escherichia coli",
#' "Klebsiella pneumoniae",
#' "Pseudomonas aeruginosa"),
#' vanc = "-", # Vancomycin
#' amox = "-", # Amoxicillin
#' coli = "-", # Colistin
#' cfta = "-", # Ceftazidime
#' cfur = "-", # Cefuroxime
#' peni = "S", # Benzylpenicillin
#' cfox = "S", # Cefoxitin
#' stringsAsFactors = FALSE)
#'
#' a
#' # mo vanc amox coli cfta cfur peni cfox
#' # 1 Staphylococcus aureus - - - - - S S
#' # 2 Enterococcus faecalis - - - - - S S
#' # 3 Escherichia coli - - - - - S S
#' # 4 Klebsiella pneumoniae - - - - - S S
#' # 5 Pseudomonas aeruginosa - - - - - S S
#'
#' b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
#'
#' b
#' # mo vanc amox coli cfta cfur peni cfox
#' # 1 Staphylococcus aureus - S R R S S S
#' # 2 Enterococcus faecalis - - R R R S R
#' # 3 Escherichia coli R - - - - R S
#' # 4 Klebsiella pneumoniae R R - - - R S
#' # 5 Pseudomonas aeruginosa R R - - R R R
EUCAST_rules <- function(tbl,
col_mo = NULL,
info = TRUE,
rules = c("breakpoints", "expert", "other", "all"),
verbose = FALSE,
amcl = 'amcl',
amik = 'amik',
amox = 'amox',
ampi = 'ampi',
azit = 'azit',
azlo = 'azlo',
aztr = 'aztr',
cefa = 'cefa',
cfep = 'cfep',
cfot = 'cfot',
cfox = 'cfox',
cfra = 'cfra',
cfta = 'cfta',
cftr = 'cftr',
cfur = 'cfur',
chlo = 'chlo',
cipr = 'cipr',
clar = 'clar',
clin = 'clin',
clox = 'clox',
coli = 'coli',
czol = 'czol',
dapt = 'dapt',
doxy = 'doxy',
erta = 'erta',
eryt = 'eryt',
fosf = 'fosf',
fusi = 'fusi',
gent = 'gent',
imip = 'imip',
kana = 'kana',
levo = 'levo',
linc = 'linc',
line = 'line',
mero = 'mero',
mezl = 'mezl',
mino = 'mino',
moxi = 'moxi',
nali = 'nali',
neom = 'neom',
neti = 'neti',
nitr = 'nitr',
norf = 'norf',
novo = 'novo',
oflo = 'oflo',
oxac = 'oxac',
peni = 'peni',
pipe = 'pipe',
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 = NULL) {
EUCAST_VERSION_BREAKPOINTS <- "8.1, 2018"
EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
if (!is.data.frame(tbl)) {
stop("`tbl` must be a data frame.", call. = FALSE)
}
# try to find columns based on type
# -- mo
if (!is.null(col_bactid)) {
col_mo <- col_bactid
warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
} else if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"]
message("NOTE: Using column `", col_mo, "` as input for `col_mo`.")
}
if (!all(rules %in% c("breakpoints", "expert", "other", "all"))) {
stop("Parameter `rules` must be one or more of: 'breakpoints', 'expert', 'other', 'all'.")
}
if (is.null(col_mo)) {
stop("Parameter `col_mo` must be set")
}
warned <- FALSE
changed_results <- 0
txt_error <- function() { cat("", bgRed(black(" ERROR ")), "\n") }
txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING ")), "\n") }; warned <<- TRUE }
txt_ok <- function() {
if (warned == FALSE) {
if (changed_results > 0) {
if (changed_results == 1) {
cat(blue(" (1 change)\n"))
} else {
cat(blue(paste0(" (", changed_results, " changes)\n")))
}
} else {
cat(green(" (no changes)\n"))
}
warned <<- 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, oxac, peni, pipe, 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]
oxac <- col.list[oxac]
peni <- col.list[peni]
pipe <- col.list[pipe]
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]
amount_changed <- 0
amount_affected_rows <- integer(0)
verbose_info <- data.frame(rule_type = character(0),
rule_set = character(0),
force_to = character(0),
found = integer(0),
changed = integer(0),
target_columns = integer(0),
target_rows = integer(0),
stringsAsFactors = FALSE)
# helper function for editing the table
edit_rsi <- function(to, rule, rows, cols) {
cols <- cols[!is.na(cols)]
if (length(rows) > 0 & length(cols) > 0) {
before <- as.character(unlist(as.list(tbl_original[rows, cols])))
tryCatch(
# insert into original table
tbl_original[rows, cols] <<- to,
warning = function(w) {
if (w$message %like% 'invalid factor level') {
warning('Value "', to, '" could not be applied to column(s) `', paste(cols, collapse = '`, `'), '` because this value is not an existing factor level.', call. = FALSE)
} else {
warning(w$message, call. = FALSE)
}
txt_warning()
},
error = function(e) {
txt_error()
stop(e, call. = FALSE)
}
)
after <- as.character(unlist(as.list(tbl_original[rows, cols])))
amount_changed <<- amount_changed + sum(before != after, na.rm = TRUE)
amount_affected_rows <<- unique(c(amount_affected_rows, rows))
changed_results <<- changed_results + sum(before != after, na.rm = TRUE) # will be reset at start of every rule
if (verbose == TRUE) {
for (i in 1:length(cols)) {
# add new row for every affected column
verbose_new <- data.frame(rule_type = rule[1],
rule_set = rule[2],
force_to = to,
found = length(before),
changed = sum(before != after, na.rm = TRUE),
target_column = cols[i],
stringsAsFactors = FALSE)
verbose_new$target_rows <- list(unname(rows))
rownames(verbose_new) <- NULL
verbose_info <<- rbind(verbose_info, verbose_new)
}
}
}
}
na.rm <- function(col) {
if (is.na(col)) {
""
} else {
col
}
}
# save original table
tbl_original <- tbl
# join to microorganisms data set
tbl <- tbl %>%
mutate_at(vars(col_mo), as.mo) %>%
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
# 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(pipe, pita, azlo, mezl)
fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
all_betalactam <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni)
if (info == TRUE) {
cat("Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)\n")
}
# since ampicillin ^= amoxicillin, get the first from the latter (not in original table)
if (!is.na(ampi) & !is.na(amox)) {
if (verbose == TRUE) {
cat(bgGreen("\n VERBOSE: transforming",
length(which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R"))),
"empty ampicillin fields to 'S' based on amoxicillin. "))
cat(bgGreen("\n VERBOSE: transforming",
length(which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R"))),
"empty ampicillin fields to 'I' based on amoxicillin. "))
cat(bgGreen("\n VERBOSE: transforming",
length(which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R"))),
"empty ampicillin fields to 'R' based on amoxicillin. \n"))
}
tbl[which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "S"
tbl[which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "I"
tbl[which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "R"
}
if (any(c("all", "breakpoints") %in% rules)) {
# BREAKPOINTS -------------------------------------------------------------
if (info == TRUE) {
cat(bold(paste0('\nEUCAST Clinical Breakpoints (v', EUCAST_VERSION_BREAKPOINTS, ')\n')))
}
rule_group <- "Breakpoints"
# Enterobacteriales (Order) ----
rule <- 'Enterobacteriales (Order)'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$order == 'Enterobacteriales'
& tbl[, ampi] == 'S'),
cols = amox)
}
if (!is.na(ampi)) {
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$order == 'Enterobacteriales'
& tbl[, ampi] == 'I'),
cols = amox)
}
if (!is.na(ampi)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$order == 'Enterobacteriales'
& tbl[, ampi] == 'R'),
cols = amox)
}
if (info == TRUE) {
txt_ok()
}
# Staphylococcus ----
rule <- italic('Staphylococcus')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(peni) & !is.na(cfox)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, peni] == 'S'
& tbl[, cfox] == 'S'),
cols = c(ampi, amox, pipe, tica))
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, peni] == 'R'
& tbl[, cfox] == 'S'),
cols = c(oxac, clox))
}
if (!is.na(cfox)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, cfox] == 'R'),
cols = all_betalactam)
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Staphylococcus saprophyticus"
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pipe, pita))
}
if (!is.na(cfox)) {
# inferred from cefoxitin
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, cfox] == 'S'),
cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)]))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, cfox] == 'I'),
cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)]))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, cfox] == 'R'),
cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)]))
}
if (!is.na(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, norf] == 'S'),
cols = c(cipr, levo, moxi, oflo))
}
if (!is.na(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, eryt] == 'S'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, eryt] == 'I'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, eryt] == 'R'),
cols = c(azit, clar, roxi))
}
if (!is.na(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Enterococcus ----
rule <- italic('Enterococcus')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(ampi)) { # penicillin group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Enterococcus faecium"
& tbl[, ampi] == 'R'),
cols = all_betalactam)
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'I'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'R'),
cols = c(amox, amcl, pipe, pita))
}
if (!is.na(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, norf] == 'S'),
cols = c(cipr, levo))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, norf] == 'I'),
cols = c(cipr, levo))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, norf] == 'R'),
cols = c(cipr, levo))
}
if (info == TRUE) {
txt_ok()
}
# Streptococcus groups A, B, C, G----
rule <- paste(italic('Streptococcus'), 'groups A, B, C, G')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, peni] == 'S'),
cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, peni] == 'I'),
cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, peni] == 'R'),
cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl))
}
if (!is.na(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, norf] == 'S'),
cols = c(levo, moxi))
}
if (!is.na(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, eryt] == 'S'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, eryt] == 'I'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, eryt] == 'R'),
cols = c(azit, clar, roxi))
}
if (!is.na(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Streptococcus pneumoniae ----
rule <- italic('Streptococcus pneumoniae')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'I'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'R'),
cols = c(amox, amcl, pipe, pita))
}
if (!is.na(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, norf] == 'S'),
cols = c(levo, moxi))
}
if (!is.na(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, eryt] == 'S'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, eryt] == 'I'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, eryt] == 'R'),
cols = c(azit, clar, roxi))
}
if (!is.na(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Viridans group streptococci ----
rule <- 'Viridans group streptococci'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
viridans_group <- c("anginosus", "australis", "bovis", "constellatus", "cristatus",
"equinus", "gallolyticus", "gordonii", "infantarius", "infantis",
"intermedius", "mitis", "mutans", "oligofermentans", "oralis",
"parasanguinis", "peroris", "pseudopneumoniae", "salivarius",
"sanguinis", "sinensis", "sobrinus", "thermophilus", "vestibularis")
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'I'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'R'),
cols = c(amox, amcl, pipe, pita))
}
if (info == TRUE) {
txt_ok()
}
# Haemophilus influenzae ----
rule <- italic('Haemophilus influenzae')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'S'),
cols = c(amox, pipe))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'I'),
cols = c(amox, pipe))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'R'),
cols = c(amox, pipe))
}
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.na(amcl)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, amcl] == 'S'),
cols = pita)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, amcl] == 'I'),
cols = pita)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, amcl] == 'R'),
cols = pita)
}
if (!is.na(nali)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, nali] == 'S'),
cols = c(cipr, levo, moxi, oflo))
}
if (!is.na(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Moraxella catarrhalis ----
rule <- italic('Moraxella catarrhalis')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(amcl)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, amcl] == 'S'),
cols = pita)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, amcl] == 'I'),
cols = pita)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, amcl] == 'R'),
cols = pita)
}
if (!is.na(nali)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, nali] == 'S'),
cols = c(cipr, levo, moxi, oflo))
}
if (!is.na(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, eryt] == 'S'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, eryt] == 'I'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, eryt] == 'R'),
cols = c(azit, clar, roxi))
}
if (!is.na(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Anaerobic Gram positives ----
rule <- 'Anaerobic Gram positives'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'S'),
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'I'),
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'R'),
cols = c(ampi, amox, pipe, pita, tica))
}
if (info == TRUE) {
txt_ok()
}
# Anaerobic Gram negatives ----
rule <- 'Anaerobic Gram negatives'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'S'),
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'I'),
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'R'),
cols = c(ampi, amox, pipe, pita, tica))
}
if (info == TRUE) {
txt_ok()
}
# Pasteurella multocida ----
rule <- italic('Pasteurella multocida')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Pasteurella multocida"
& tbl[, peni] == 'S'),
cols = c(ampi, amox))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Pasteurella multocida"
& tbl[, peni] == 'I'),
cols = c(ampi, amox))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Pasteurella multocida"
& tbl[, peni] == 'R'),
cols = c(ampi, amox))
}
if (info == TRUE) {
txt_ok()
}
# Campylobacter jejuni and coli ----
rule <- paste(italic('Campylobacter jejuni'), 'and', italic('C. coli'))
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'S'),
cols = c(azit, clar))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'I'),
cols = c(azit, clar))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'R'),
cols = c(azit, clar))
}
if (!is.na(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'S'),
cols = doxy)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'I'),
cols = doxy)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'R'),
cols = doxy)
}
if (info == TRUE) {
txt_ok()
}
# Aerococcus sanguinicola/urinae ----
rule <- paste(italic('Aerococcus sanguinicola'), 'and', italic('A. urinae'))
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'S'),
cols = fluoroquinolones)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'I'),
cols = fluoroquinolones)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'R'),
cols = fluoroquinolones)
}
if (!is.na(cipr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, cipr] == 'S'),
cols = levo)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, cipr] == 'I'),
cols = levo)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, cipr] == 'R'),
cols = levo)
}
if (info == TRUE) {
txt_ok()
}
# Kingella kingae ----
rule <- italic('Kingella kingae')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, peni] == 'S'),
cols = c(ampi, amox))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, peni] == 'I'),
cols = c(ampi, amox))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, peni] == 'R'),
cols = c(ampi, amox))
}
if (!is.na(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, eryt] == 'S'),
cols = c(azit, clar))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, eryt] == 'I'),
cols = c(azit, clar))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, eryt] == 'R'),
cols = c(azit, clar))
}
if (!is.na(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, tetr] == 'S'),
cols = doxy)
}
if (info == TRUE) {
txt_ok()
}
} # end of breakpoints
if (any(c("all", "expert") %in% rules)) {
# EXPERT RULES AND INTRINSIC RESISTANCE -----------------------------------
if (info == TRUE) {
cat(bold(paste0('\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v', EUCAST_VERSION_EXPERT_RULES, ')\n')))
}
rule_group <- "Expert Rules"
# Table 1: Intrinsic resistance in Enterobacteriaceae ----
rule <- paste('Table 1: Intrinsic resistance in', italic('Enterobacteriaceae'))
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# Intrinsic R for this group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'),
cols = c(peni, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
# Citrobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
cols = c(aminopenicillins, tica))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Enterobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
cols = c(aminopenicillins, amcl, czol, cfox))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Escherichia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Escherichia hermanni'),
cols = c(aminopenicillins, tica))
# Hafnia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Hafnia alvei'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Klebsiella
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Klebsiella'),
cols = c(aminopenicillins, tica))
# Morganella / Proteus
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Morganella morganii'),
cols = c(aminopenicillins, amcl, czol, tetracyclines, polymyxins, nitr))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Proteus mirabilis'),
cols = c(tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Proteus penneri'),
cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Proteus vulgaris'),
cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
# Providencia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Providencia rettgeri'),
cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Providencia stuartii'),
cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
# Raoultella
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Raoultella'),
cols = c(aminopenicillins, tica))
# Serratia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Serratia marcescens'),
cols = c(aminopenicillins, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != na.rm(mino)], polymyxins, nitr))
# Yersinia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
cols = c(aminopenicillins, amcl, tica, czol, cfox))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
cols = c(poly, coli))
if (info == TRUE) {
txt_ok()
}
# Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria ----
rule <- 'Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# Intrinsic R for this group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$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',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
cols = c(aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != na.rm(mino)]))
# Achromobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
cols = c(aminopenicillins, czol, cfot, cftr, erta))
# Burkholderia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
# the 'Burkholderia cepacia complex' are all these species: (PMID 16217180)
rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins))
# Elizabethkingia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$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',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
# Pseudomonas
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
cols = c(aminopenicillins, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
# Stenotrophomonas
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr))
if (info == TRUE) {
txt_ok()
}
# Table 3: Intrinsic resistance in other Gram-negative bacteria ----
rule <- 'Table 3: Intrinsic resistance in other Gram-negative bacteria'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# Intrinsic R for this group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c('Haemophilus',
'Moraxella',
'Neisseria',
'Campylobacter')),
cols = c(glycopeptides, linc, dapt, line))
# Haemophilus
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Haemophilus influenzae'),
cols = c(fusi, streptogramins))
# Moraxella
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Moraxella catarrhalis'),
cols = trim)
# Neisseria
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Neisseria'),
cols = trim)
# Campylobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Campylobacter fetus'),
cols = c(fusi, streptogramins, trim, nali))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Campylobacter (jejuni|coli)'),
cols = c(fusi, streptogramins, trim))
if (info == TRUE) {
txt_ok()
}
# Table 4: Intrinsic resistance in Gram-positive bacteria ----
rule <- 'Table 4: Intrinsic resistance in Gram-positive bacteria'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# Intrinsic R for this group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$gramstain == "Gram positive"),
cols = c(aztr, polymyxins, nali))
# Staphylococcus
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Staphylococcus saprophyticus'),
cols = c(fusi, cfta, fosf, novo))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Staphylococcus (cohnii|xylosus)'),
cols = c(cfta, novo))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Staphylococcus capitis'),
cols = c(cfta, fosf))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
cols = cfta)
# Streptococcus
# rule 4.5
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Streptococcus'),
cols = c(fusi, aminoglycosides))
# Enterococcus
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterococcus faecalis'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, clin, qida, trim, trsu))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterococcus (gallinarum|casseliflavus)'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, clin, qida, vanc, trim, trsu))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterococcus faecium'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, trim, trsu))
# Corynebacterium
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Corynebacterium'),
cols = fosf)
# Listeria
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Listeria monocytogenes'),
cols = c(cfta, cephalosporins[cephalosporins != na.rm(cfta)]))
# other
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c('Leuconostoc', 'Pediococcus')),
cols = glycopeptides)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Lactobacillus'),
cols = glycopeptides)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Clostridium (ramosum|innocuum)'),
cols = vanc)
if (info == TRUE) {
txt_ok()
}
# Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci ----
rule <- 'Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 8.3
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)'
& tbl[, peni] == 'S'),
cols = c(aminopenicillins, cephalosporins, carbapenems))
}
# rule 8.6
if (!is.na(ampi)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Enterococcus'
& tbl[, ampi] == 'R'),
cols = c(ureidopenicillins, carbapenems))
}
if (!is.na(amox)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Enterococcus'
& tbl[, amox] == 'R'),
cols = c(ureidopenicillins, carbapenems))
}
if (info == TRUE) {
txt_ok()
}
# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
rule <- 'Table 9: Interpretive rules for B-lactam agents and Gram-negative rods'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 9.3
if (!is.na(tica) & !is.na(pipe)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, tica] == 'R'
& tbl[, pipe] == 'S'),
cols = pipe)
}
if (info == TRUE) {
txt_ok()
}
# Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria ----
rule <- 'Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 10.2
# if (!is.na(ampi)) {
# you should know first if the are B-lactamase positive, so do not run for now
# edit_rsi(to = 'R',
# rule = c(rule_group, rule),
# rows = which(tbl$fullname %like% '^Haemophilus influenza'
# & tbl[, ampi] == 'R'),
# cols = c(ampi, amox, amcl, pipe, pita, cfur))
# }
if (info == TRUE) {
txt_ok()
}
# Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins ----
rule <- 'Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 11.1
if (!is.na(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, eryt] == 'S'),
cols = c(azit, clar))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl[, eryt] == 'I'),
cols = c(azit, clar))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, eryt] == 'R'),
cols = c(azit, clar))
}
if (info == TRUE) {
txt_ok()
}
# Table 12: Interpretive rules for aminoglycosides ----
rule <- 'Table 12: Interpretive rules for aminoglycosides'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 12.2
if (!is.na(tobr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, tobr] == 'R'),
cols = c(kana, amik))
}
# rule 12.3
if (!is.na(gent)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, gent] == 'R'),
cols = aminoglycosides)
}
# rule 12.8
if (!is.na(gent) & !is.na(tobr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, gent] == 'I'
& tbl[, tobr] == 'S'),
cols = gent)
}
# rule 12.9
if (!is.na(gent) & !is.na(tobr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, tobr] == 'I'
& tbl[, gent] == 'R'),
cols = tobr)
}
if (info == TRUE) {
txt_ok()
}
# Table 13: Interpretive rules for quinolones ----
rule <- 'Table 13: Interpretive rules for quinolones'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 13.2
if (!is.na(moxi)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, moxi] == 'R'),
cols = fluoroquinolones)
}
# rule 13.4
if (!is.na(moxi)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Streptococcus pneumoniae'
& tbl[, moxi] == 'R'),
cols = fluoroquinolones)
}
# rule 13.5
if (!is.na(cipr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, cipr] == 'R'),
cols = fluoroquinolones)
}
# rule 13.8
if (!is.na(cipr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Neisseria gonorrhoeae'
& tbl[, cipr] == 'R'),
cols = fluoroquinolones)
}
if (info == TRUE) {
txt_ok()
}
} # end of expert rules
if (any(c("all", "other") %in% rules)) {
# OTHER RULES -------------------------------------------------------------
if (info == TRUE) {
cat(bold('\nOther rules\n'))
}
rule_group <- "Other rules"
rule <- 'Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(amcl)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, amcl] == 'R'),
cols = ampi)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(pita)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, pita] == 'R'),
cols = pipe)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(trsu)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, trsu] == 'R'),
cols = trim)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, ampi] == 'S'),
cols = amcl)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(pipe)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, pipe] == 'S'),
cols = pita)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(trim)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, trim] == 'S'),
cols = trsu)
}
if (info == TRUE) {
txt_ok()
}
} # end of other rules
# restore old col_mo values if needed
# if (!is.null(col_mo_original)) {
# tbl_original[, col_mo] <- col_mo_original
# }
if (info == TRUE) {
if (verbose == TRUE) {
wouldve <- "would have "
} else {
wouldve <- ""
}
if (amount_changed == 0) {
colour <- green
} else {
colour <- blue
}
cat(bold('\n=> EUCAST rules affected',
amount_affected_rows %>% length() %>% format(big.mark = ","),
'out of', nrow(tbl_original) %>% format(big.mark = ","),
'rows ->',
colour(paste0(wouldve, 'changed'),
amount_changed %>% format(big.mark = ","), 'test results.\n\n')))
}
if (verbose == TRUE) {
return(verbose_info)
}
tbl_original
}
#' @rdname EUCAST
#' @export
interpretive_reading <- function(...) {
EUCAST_rules(...)
}
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