# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # AUTHORS # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # # LICENCE # # This package 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 R package 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 version 2.0 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 Antibiotics #' @param col_bactid deprecated, use \code{col_mo} instead. #' @param ... parameters that are passed on to \code{eucast_rules} #' @inheritParams first_isolate #' @section Antibiotics: #' To define antibiotics column names, input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning. #' #' 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_rules #' @export #' @importFrom dplyr %>% select pull mutate_at vars #' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style #' @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 = strip_style(rule[1]), rule_set = strip_style(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(paste('\n=> EUCAST rules', paste0(wouldve, '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_rules #' @export EUCAST_rules <- function(...) { .Deprecated("eucast_rules") eucast_rules(...) } #' @rdname eucast_rules #' @export interpretive_reading <- function(...) { .Deprecated("eucast_rules") eucast_rules(...) }