AMR/R/eucast.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
#                                                                      #
# AUTHORS                                                              #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)           #
#                                                                      #
# LICENCE                                                              #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0,    #
# as published by the Free Software Foundation.                        #
#                                                                      #
# This program is distributed in the hope that it will be useful,      #
# but WITHOUT ANY WARRANTY; without even the implied warranty of       #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the        #
# GNU General Public License for more details.                         #
# ==================================================================== #

#' EUCAST expert rules
#'
#' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
#' @param col_mo column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}
#' @param info print progress
#' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,peni,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.
#' @param col_bactid Deprecated. Use \code{col_mo} instead.
#' @param ... parameters that are passed on to \code{EUCAST_rules}
#' @section Antibiotics:
#' Abbrevations of the column containing antibiotics:
#'
#'  \strong{amcl}: amoxicillin and beta-lactamase inhibitor (\emph{J01CR02}),
#'  \strong{amik}: amikacin (\emph{J01GB06}),
#'  \strong{amox}: amoxicillin (\emph{J01CA04}),
#'  \strong{ampi}: ampicillin (\emph{J01CA01}),
#'  \strong{azit}: azithromycin (\emph{J01FA10}),
#'  \strong{azlo}: azlocillin (\emph{J01CA09}),
#'  \strong{aztr}: aztreonam (\emph{J01DF01}),
#'  \strong{cefa}: cefaloridine (\emph{J01DB02}),
#'  \strong{cfep}: cefepime (\emph{J01DE01}),
#'  \strong{cfot}: cefotaxime (\emph{J01DD01}),
#'  \strong{cfox}: cefoxitin (\emph{J01DC01}),
#'  \strong{cfra}: cefradine (\emph{J01DB09}),
#'  \strong{cfta}: ceftazidime (\emph{J01DD02}),
#'  \strong{cftr}: ceftriaxone (\emph{J01DD04}),
#'  \strong{cfur}: cefuroxime (\emph{J01DC02}),
#'  \strong{chlo}: chloramphenicol (\emph{J01BA01}),
#'  \strong{cipr}: ciprofloxacin (\emph{J01MA02}),
#'  \strong{clar}: clarithromycin (\emph{J01FA09}),
#'  \strong{clin}: clindamycin (\emph{J01FF01}),
#'  \strong{clox}: flucloxacillin (\emph{J01CF05}),
#'  \strong{coli}: colistin (\emph{J01XB01}),
#'  \strong{czol}: cefazolin (\emph{J01DB04}),
#'  \strong{dapt}: daptomycin (\emph{J01XX09}),
#'  \strong{doxy}: doxycycline (\emph{J01AA02}),
#'  \strong{erta}: ertapenem (\emph{J01DH03}),
#'  \strong{eryt}: erythromycin (\emph{J01FA01}),
#'  \strong{fosf}: fosfomycin (\emph{J01XX01}),
#'  \strong{fusi}: fusidic acid (\emph{J01XC01}),
#'  \strong{gent}: gentamicin (\emph{J01GB03}),
#'  \strong{imip}: imipenem and cilastatin (\emph{J01DH51}),
#'  \strong{kana}: kanamycin (\emph{J01GB04}),
#'  \strong{levo}: levofloxacin (\emph{J01MA12}),
#'  \strong{linc}: lincomycin (\emph{J01FF02}),
#'  \strong{line}: linezolid (\emph{J01XX08}),
#'  \strong{mero}: meropenem (\emph{J01DH02}),
#'  \strong{mezl}: mezlocillin (\emph{J01CA10}),
#'  \strong{mino}: minocycline (\emph{J01AA08}),
#'  \strong{moxi}: moxifloxacin (\emph{J01MA14}),
#'  \strong{nali}: nalidixic acid (\emph{J01MB02}),
#'  \strong{neom}: neomycin (\emph{J01GB05}),
#'  \strong{neti}: netilmicin (\emph{J01GB07}),
#'  \strong{nitr}: nitrofurantoin (\emph{J01XE01}),
#'  \strong{norf}: norfloxacin (\emph{J01MA06}),
#'  \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
#'  \strong{oflo}: ofloxacin (\emph{J01MA01}),
#'  \strong{peni}: penicillins, combinations with other antibacterials (\emph{J01RA01}),
#'  \strong{pita}: piperacillin and beta-lactamase inhibitor (\emph{J01CR05}),
#'  \strong{poly}: polymyxin B (\emph{J01XB02}),
#'  \strong{pris}: pristinamycin (\emph{J01FG01}),
#'  \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
#'  \strong{rifa}: rifampicin (\emph{J04AB02}),
#'  \strong{roxi}: roxithromycin (\emph{J01FA06}),
#'  \strong{siso}: sisomicin (\emph{J01GB08}),
#'  \strong{teic}: teicoplanin (\emph{J01XA02}),
#'  \strong{tetr}: tetracycline (\emph{J01AA07}),
#'  \strong{tica}: ticarcillin (\emph{J01CA13}),
#'  \strong{tige}: tigecycline (\emph{J01AA12}),
#'  \strong{tobr}: tobramycin (\emph{J01GB01}),
#'  \strong{trim}: trimethoprim (\emph{J01EA01}),
#'  \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
#'  \strong{vanc}: vancomycin (\emph{J01XA01}).
#' @keywords interpretive eucast reading resistance
#' @rdname EUCAST
#' @export
#' @importFrom dplyr %>% left_join select
#' @return table with edited variables of antibiotics.
#' @source
#'   EUCAST Expert Rules Version 2.0: \cr
#'   Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
#'   \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x} \cr
#'   \cr
#'   EUCAST Expert Rules Version 3.1 (Intrinsic Resistance and Exceptional Phenotypes Tables): \cr
#'   \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
#' @examples
#' a <- EUCAST_rules(septic_patients)
#' a <- data.frame(mo = c("STAAUR",  # Staphylococcus aureus
#'                        "ENCFAE",  # Enterococcus faecalis
#'                        "ESCCOL",  # Escherichia coli
#'                        "KLEPNE",  # Klebsiella pneumoniae
#'                        "PSEAER"), # Pseudomonas aeruginosa
#'                 vanc = "-",       # Vancomycin
#'                 amox = "-",       # Amoxicillin
#'                 coli = "-",       # Colistin
#'                 cfta = "-",       # Ceftazidime
#'                 cfur = "-",       # Cefuroxime
#'                 stringsAsFactors = FALSE)
#' a
#'
#' b <- EUCAST_rules(a)
#' b
EUCAST_rules <- function(tbl,
                         col_mo = 'mo',
                         info = TRUE,
                         amcl = 'amcl',
                         amik = 'amik',
                         amox = 'amox',
                         ampi = 'ampi',
                         azit = 'azit',
                         azlo = 'azlo',
                         aztr = 'aztr',
                         cefa = 'cefa',
                         cfep = 'cfep',
                         cfot = 'cfot',
                         cfox = 'cfox',
                         cfra = 'cfra',
                         cfta = 'cfta',
                         cftr = 'cftr',
                         cfur = 'cfur',
                         chlo = 'chlo',
                         cipr = 'cipr',
                         clar = 'clar',
                         clin = 'clin',
                         clox = 'clox',
                         coli = 'coli',
                         czol = 'czol',
                         dapt = 'dapt',
                         doxy = 'doxy',
                         erta = 'erta',
                         eryt = 'eryt',
                         fosf = 'fosf',
                         fusi = 'fusi',
                         gent = 'gent',
                         imip = 'imip',
                         kana = 'kana',
                         levo = 'levo',
                         linc = 'linc',
                         line = 'line',
                         mero = 'mero',
                         mezl = 'mezl',
                         mino = 'mino',
                         moxi = 'moxi',
                         nali = 'nali',
                         neom = 'neom',
                         neti = 'neti',
                         nitr = 'nitr',
                         norf = 'norf',
                         novo = 'novo',
                         oflo = 'oflo',
                         peni = 'peni',
                         pita = 'pita',
                         poly = 'poly',
                         pris = 'pris',
                         qida = 'qida',
                         rifa = 'rifa',
                         roxi = 'roxi',
                         siso = 'siso',
                         teic = 'teic',
                         tetr = 'tetr',
                         tica = 'tica',
                         tige = 'tige',
                         tobr = 'tobr',
                         trim = 'trim',
                         trsu = 'trsu',
                         vanc = 'vanc',
                         col_bactid = 'bactid') {

  EUCAST_VERSION <- "3.1"

  if (col_bactid %in% colnames(tbl)) {
    col_mo <- col_bactid
    warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
  }
  if (!col_mo %in% colnames(tbl)) {
    stop('Column ', col_mo, ' not found.', call. = FALSE)
  }

  # check columns
  col.list <- c(amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot,
                cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
                czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
                levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr,
                novo, norf, oflo, peni, pita, poly, pris,  qida, rifa, roxi, siso,
                teic, tetr, tica, tige, tobr, trim, trsu, vanc)
  col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
  amcl <- col.list[amcl]
  amik <- col.list[amik]
  amox <- col.list[amox]
  ampi <- col.list[ampi]
  azit <- col.list[azit]
  azlo <- col.list[azlo]
  aztr <- col.list[aztr]
  cefa <- col.list[cefa]
  cfep <- col.list[cfep]
  cfot <- col.list[cfot]
  cfox <- col.list[cfox]
  cfra <- col.list[cfra]
  cfta <- col.list[cfta]
  cftr <- col.list[cftr]
  cfur <- col.list[cfur]
  chlo <- col.list[chlo]
  cipr <- col.list[cipr]
  clar <- col.list[clar]
  clin <- col.list[clin]
  clox <- col.list[clox]
  coli <- col.list[coli]
  czol <- col.list[czol]
  dapt <- col.list[dapt]
  doxy <- col.list[doxy]
  erta <- col.list[erta]
  eryt <- col.list[eryt]
  fosf <- col.list[fosf]
  fusi <- col.list[fusi]
  gent <- col.list[gent]
  imip <- col.list[imip]
  kana <- col.list[kana]
  levo <- col.list[levo]
  linc <- col.list[linc]
  line <- col.list[line]
  mero <- col.list[mero]
  mezl <- col.list[mezl]
  mino <- col.list[mino]
  moxi <- col.list[moxi]
  nali <- col.list[nali]
  neom <- col.list[neom]
  neti <- col.list[neti]
  nitr <- col.list[nitr]
  norf <- col.list[norf]
  novo <- col.list[novo]
  oflo <- col.list[oflo]
  peni <- col.list[peni]
  pita <- col.list[pita]
  poly <- col.list[poly]
  pris <- col.list[pris]
  qida <- col.list[qida]
  rifa <- col.list[rifa]
  roxi <- col.list[roxi]
  siso <- col.list[siso]
  teic <- col.list[teic]
  tetr <- col.list[tetr]
  tica <- col.list[tica]
  tige <- col.list[tige]
  tobr <- col.list[tobr]
  trim <- col.list[trim]
  trsu <- col.list[trsu]
  vanc <- col.list[vanc]

  total <- 0
  total_rows <- integer(0)

  # helper function for editing the table
  edit_rsi <- function(to, rows, cols, EUCAST_rule = "") {
    # later: use this as attribute for the edited observations
    EUCAST_rule <- trimws(paste("EUCAST rule", EUCAST_rule))
    cols <- cols[!is.na(cols)]
    if (length(rows) > 0 & length(cols) > 0) {
      tbl[rows, cols] <<- to
      total <<- total + (length(rows) * length(cols))
      total_rows <<- c(total_rows, rows)
    }
  }

  # join to microorganisms data set
  col_mo_original <- NULL
  if (!tbl %>% pull(col_mo) %>% is.mo()) {
    col_mo_original <- tbl %>% pull(col_mo)
    tbl[, col_mo] <- as.mo(tbl[, col_mo])
  }
  tbl <- tbl %>% left_join_microorganisms(by = col_mo, suffix = c("_tempmicroorganisms", ""))

  # antibiotic classes
  aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
  tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart
  polymyxins <- c(poly, coli)
  macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clinda is set apart
  glycopeptides <- c(vanc, teic)
  streptogramins <- c(qida, pris) # should officially also be quinupristin/dalfopristin
  cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
  carbapenems <- c(erta, imip, mero)
  aminopenicillins <- c(ampi, amox)
  ureidopenicillins <- c(pita, azlo, mezl)
  fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)

  if (info == TRUE) {
    cat(
      paste0(
        '\nApplying rules to ',
        tbl[!is.na(tbl$genus),] %>% nrow() %>% format(big.mark = ","),
        ' rows according to "EUCAST Expert Rules Version ', EUCAST_VERSION, '"\n')
    )
  }

  # Table 1: Intrinsic resistance in Enterobacteriaceae ----
  if (info == TRUE) {
    cat('- Table 1:  Intrinsic resistance in Enterobacteriaceae\n')
  }
  # Intrisiek R for this group
  edit_rsi(to = 'R',
           rows = which(tbl$family == 'Enterobacteriaceae'),
           cols = c(peni, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
  # Citrobacter
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
           cols = c(aminopenicillins, tica))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
           cols = c(aminopenicillins, amcl, czol, cfox))
  # Enterobacter
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
           cols = c(aminopenicillins, amcl, czol, cfox))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
           cols = c(aminopenicillins, amcl, czol, cfox))
  # Escherichia
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Escherichia hermanni'),
           cols = c(aminopenicillins, tica))
  # Hafnia
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Hafnia alvei'),
           cols = c(aminopenicillins, amcl, czol, cfox))
  # Klebsiella
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Klebsiella'),
           cols = c(aminopenicillins, tica))
  # Morganella / Proteus
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Morganella morganii'),
           cols = c(aminopenicillins, amcl, czol, tetracyclines, polymyxins, nitr))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Proteus mirabilis'),
           cols = c(tetracyclines, tige, polymyxins, nitr))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Proteus penneri'),
           cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Proteus vulgaris'),
           cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
  # Providencia
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Providencia rettgeri'),
           cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Providencia stuartii'),
           cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
  # Raoultella
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Raoultella'),
           cols = c(aminopenicillins, tica))
  # Serratia
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Serratia marcescens'),
           cols = c(aminopenicillins, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxins, nitr))
  # Yersinia
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
           cols = c(aminopenicillins, amcl, tica, czol, cfox))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
           cols = c(poly, coli))


  # Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria ----
  if (info == TRUE) {
    cat('- Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria\n')
  }
  # Intrisiek R for this group
  edit_rsi(to = 'R',
           rows = which(tbl$genus %in% c('Achromobacter',
                                         'Acinetobacter',
                                         'Alcaligenes',
                                         'Bordatella',
                                         'Burkholderia',
                                         'Elizabethkingia',
                                         'Flavobacterium',
                                         'Ochrobactrum',
                                         'Pseudomonas',
                                         'Stenotrophomonas')),
           cols = c(peni, cfox, cfur, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
  # Acinetobacter
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
           cols = c(aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
  # Achromobacter
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
           cols = c(aminopenicillins, czol, cfot, cftr, erta))
  # Burkholderia
  edit_rsi(to = 'R',
           # onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
           rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
           cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins))
  # Elizabethkingia
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
           cols = c(aminopenicillins, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxins))
  # Ochrobactrum
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
           cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
  # Pseudomonas
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
           cols = c(aminopenicillins, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
  # Stenotrophomonas
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
           cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr))


  # Table 3: Intrinsic resistance in other Gram-negative bacteria ----
  if (info == TRUE) {
    cat('- Table 3:  Intrinsic resistance in other Gram-negative bacteria\n')
  }
  # Intrisiek R for this group
  edit_rsi(to = 'R',
           rows = which(tbl$genus %in% c('Haemophilus',
                                         'Moraxella',
                                         'Neisseria',
                                         'Campylobacter')),
           cols = c(glycopeptides, linc, dapt, line))
  # Haemophilus
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Haemophilus influenzae'),
           cols = c(fusi, streptogramins))
  # Moraxella
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Moraxella catarrhalis'),
           cols = trim)
  # Neisseria
  edit_rsi(to = 'R',
           rows = which(tbl$genus == 'Neisseria'),
           cols = trim)
  # Campylobacter
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Campylobacter fetus'),
           cols = c(fusi, streptogramins, trim, nali))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Campylobacter (jejuni|coli)'),
           cols = c(fusi, streptogramins, trim))


  # Table 4: Intrinsic resistance in Gram-positive bacteria ----
  if (info == TRUE) {
    cat('- Table 4:  Intrinsic resistance in Gram-positive bacteria\n')
  }
  # Intrisiek R for this group
  edit_rsi(to = 'R',
           rows = which(tbl$gramstain %like% 'Positi(e|)(v|f)'),
           cols = c(aztr, polymyxins, nali))
  # Staphylococcus
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Staphylococcus saprophyticus'),
           cols = c(fusi, cfta, fosf, novo))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Staphylococcus (cohnii|xylosus)'),
           cols = c(cfta, novo))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Staphylococcus capitis'),
           cols = c(cfta, fosf))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
           cols = cfta)
  # Streptococcus
  edit_rsi(to = 'R',
           rows = which(tbl$genus == 'Streptococcus'),
           cols = c(fusi, cfta, aminoglycosides))
  # Enterococcus
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Enterococcus faecalis'),
           cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, clin, qida, trim, trsu))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Enterococcus (gallinarum|casseliflavus)'),
           cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, clin, qida, vanc, trim, trsu))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Enterococcus faecium'),
           cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, trim, trsu))
  # Corynebacterium
  edit_rsi(to = 'R',
           rows = which(tbl$genus == 'Corynebacterium'),
           cols = fosf)
  # Listeria
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Listeria monocytogenes'),
           cols = c(cfta, cephalosporins[cephalosporins != cfta]))
  # overig
  edit_rsi(to = 'R',
           rows = which(tbl$genus %in% c('Leuconostoc', 'Pediococcus')),
           cols = c(vanc, teic))
  edit_rsi(to = 'R',
           rows = which(tbl$genus == 'Lactobacillus'),
           cols = c(vanc, teic))
  edit_rsi(to = 'R',
           rows = which(tbl$fullname %like% '^Clostridium (ramosum|innocuum)'),
           cols = vanc)

  # Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci ----
  if (info == TRUE) {
    cat('- Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci\n')
  }
  # rule 8.3
  if (!is.na(peni)) {
    edit_rsi(to = 'S',
             rows = which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|dysgalactiae|groep A|groep B|groep C|groep G)'
                          & tbl[, peni] == 'S'),
             cols = c(aminopenicillins, cephalosporins, carbapenems))
  }
  # rule 8.6
  if (!is.na(ampi)) {
    edit_rsi(to = 'R',
             rows = which(tbl$genus == 'Enterococcus'
                          & tbl[, ampi] == 'R'),
             cols = c(ureidopenicillins, carbapenems))
  }
  if (!is.na(amox)) {
    edit_rsi(to = 'R',
             rows = which(tbl$genus == 'Enterococcus'
                          & tbl[, amox] == 'R'),
             cols = c(ureidopenicillins, carbapenems))
  }

  # Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
  if (info == TRUE) {
    cat('- Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods\n')
  }
  # rule 9.3
  if (!is.na(tica) & !is.na(pita)) {
    edit_rsi(to = 'R',
             rows = which(tbl$family == 'Enterobacteriaceae'
                          & tbl[, tica] == 'R'
                          & tbl[, pita] == 'S'),
             cols = pita)
  }

  # Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria ----
  if (info == TRUE) {
    cat('- Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria\n')
  }
  # rule 10.2
  if (!is.na(ampi)) {
    # you should know first if the are B-lactamase positive, so do not run for now
    # edit_rsi(to = 'R',
    #          rows = which(tbl$fullname %like% '^Haemophilus influenza'
    #                       & tbl[, ampi] == 'R'),
    #          cols = c(ampi, amox, amcl, pita, cfur))
  }

  # Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins ----
  if (info == TRUE) {
    cat('- Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins\n')
  }
  # rule 11.1
  if (!is.na(eryt)) {
    if (!is.na(azit)) {
      tbl[, azit] <- tbl[, eryt]
    }
    if (!is.na(clar)) {
      tbl[, clar] <- tbl[, eryt]
    }
  }

  # Table 12: Interpretive rules for aminoglycosides ----
  if (info == TRUE) {
    cat('- Table 12: Interpretive rules for aminoglycosides\n')
  }
  # rule 12.2
  if (!is.na(tobr)) {
    edit_rsi(to = 'R',
             rows = which(tbl$genus == 'Staphylococcus'
                          & tbl[, tobr] == 'R'),
             cols = c(kana, amik))
  }
  # rule 12.3
  if (!is.na(gent)) {
    edit_rsi(to = 'R',
             rows = which(tbl$genus == 'Staphylococcus'
                          & tbl[, gent] == 'R'),
             cols = aminoglycosides)
  }
  # rule 12.8
  if (!is.na(gent) & !is.na(tobr)) {
    edit_rsi(to = 'R',
             rows = which(tbl$family == 'Enterobacteriaceae'
                          & tbl[, gent] == 'I'
                          & tbl[, tobr] == 'S'),
             cols = gent)
  }
  # rule 12.9
  if (!is.na(gent) & !is.na(tobr)) {
    edit_rsi(to = 'R',
             rows = which(tbl$family == 'Enterobacteriaceae'
                          & tbl[, tobr] == 'I'
                          & tbl[, gent] == 'R'),
             cols = tobr)
  }


  # Table 13: Interpretive rules for quinolones ----
  if (info == TRUE) {
    cat('- Table 13: Interpretive rules for quinolones\n')
  }
  # rule 13.2
  if (!is.na(moxi)) {
    edit_rsi(to = 'R',
             rows = which(tbl$genus == 'Staphylococcus'
                          & tbl[, moxi] == 'R'),
             cols = fluoroquinolones)
  }
  # rule 13.4
  if (!is.na(moxi)) {
    edit_rsi(to = 'R',
             rows = which(tbl$fullname %like% '^Streptococcus pneumoniae'
                          & tbl[, moxi] == 'R'),
             cols = fluoroquinolones)
  }
  # rule 13.5
  if (!is.na(cipr)) {
    edit_rsi(to = 'R',
             rows = which(tbl$family == 'Enterobacteriaceae'
                          & tbl[, cipr] == 'R'),
             cols = fluoroquinolones)
  }
  # rule 13.8
  if (!is.na(cipr)) {
    edit_rsi(to = 'R',
             rows = which(tbl$fullname %like% '^Neisseria gonorrhoeae'
                          & tbl[, cipr] == 'R'),
             cols = fluoroquinolones)
  }


  # Other ----
  if (info == TRUE) {
    cat('- Non-EUCAST: trim = R where trsu = R and ampi = R where amcl = R\n')
  }
  if (!is.na(amcl)) {
    edit_rsi(to = 'R',
             rows = which(tbl[, amcl] == 'R'),
             cols = ampi)
  }
  if (!is.na(trsu)) {
    edit_rsi(to = 'R',
             rows = which(tbl[, trsu] == 'R'),
             cols = trim)
  }
  if (info == TRUE) {
    cat('- Non-EUCAST: trsu = S where trim = S and amcl = S where ampi = S\n')
  }
  if (!is.na(amcl)) {
    edit_rsi(to = 'S',
             rows = which(tbl[, ampi] == 'S'),
             cols = amcl)
  }
  if (!is.na(trsu)) {
    edit_rsi(to = 'S',
             rows = which(tbl[, trim] == 'S'),
             cols = trsu)
  }
  # amox = ampi
  if (!is.na(ampi) & !is.na(amox)) {
    tbl[, amox] <- tbl %>% pull(ampi)
  }

  # Remove added columns again
  microorganisms.ncol <- ncol(AMR::microorganisms) - 2
  tbl.ncol <- ncol(tbl)
  tbl <- tbl %>% select(-c((tbl.ncol - microorganisms.ncol):tbl.ncol))
  # and remove added suffices
  colnames(tbl) <- gsub("_tempmicroorganisms", "", colnames(tbl))
  # restore old col_mo values if needed
  if (!is.null(col_mo_original)) {
    tbl[, col_mo] <- col_mo_original
  }

  if (info == TRUE) {
    cat('Done.\n\nEUCAST Expert rules applied to',
        total_rows %>% unique() %>% length() %>% format(big.mark = ","),
        'different rows; overwritten a total of',
        total %>% format(big.mark = ","), 'test results.\n\n')
  }

  tbl
}

#' @rdname EUCAST
#' @export
interpretive_reading <- function(...) {
  EUCAST_rules(...)
}