Determine multidrug-resistant organisms (MDRO)

Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.

mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
  amcl = guess_ab_col(), amik = guess_ab_col(),
  amox = guess_ab_col(), ampi = guess_ab_col(),
  azit = guess_ab_col(), aztr = guess_ab_col(),
  cefa = guess_ab_col(), cfra = guess_ab_col(),
  cfep = guess_ab_col(), cfot = guess_ab_col(),
  cfox = guess_ab_col(), cfta = guess_ab_col(),
  cftr = guess_ab_col(), cfur = guess_ab_col(),
  chlo = guess_ab_col(), cipr = guess_ab_col(),
  clar = guess_ab_col(), clin = guess_ab_col(),
  clox = guess_ab_col(), coli = guess_ab_col(),
  czol = guess_ab_col(), dapt = guess_ab_col(),
  doxy = guess_ab_col(), erta = guess_ab_col(),
  eryt = guess_ab_col(), fosf = guess_ab_col(),
  fusi = guess_ab_col(), gent = guess_ab_col(),
  imip = guess_ab_col(), kana = guess_ab_col(),
  levo = guess_ab_col(), linc = guess_ab_col(),
  line = guess_ab_col(), mero = guess_ab_col(),
  metr = guess_ab_col(), mino = guess_ab_col(),
  moxi = guess_ab_col(), nali = guess_ab_col(),
  neom = guess_ab_col(), neti = guess_ab_col(),
  nitr = guess_ab_col(), novo = guess_ab_col(),
  norf = guess_ab_col(), oflo = guess_ab_col(),
  peni = guess_ab_col(), pipe = guess_ab_col(),
  pita = guess_ab_col(), poly = guess_ab_col(),
  qida = guess_ab_col(), rifa = guess_ab_col(),
  roxi = guess_ab_col(), siso = guess_ab_col(),
  teic = guess_ab_col(), tetr = guess_ab_col(),
  tica = guess_ab_col(), tige = guess_ab_col(),
  tobr = guess_ab_col(), trim = guess_ab_col(),
  trsu = guess_ab_col(), vanc = guess_ab_col())

brmo(..., country = "nl")

mrgn(tbl, country = "de", ...)

eucast_exceptional_phenotypes(tbl, country = "EUCAST", ...)

Arguments

tbl	table with antibiotic columns, like e.g. `amox` and `amcl`
country	country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the list of ISO 3166-1 alpha-2 country codes. Case-insensitive. Currently supported are `de` (Germany) and `nl` (the Netherlands).
col_mo	column name of the unique IDs of the microorganisms (see `mo`), defaults to the first column of class `mo`. Values will be coerced using `as.mo`.
info	print progress
amcl	column name of an antibiotic, see Antibiotics
amik	column name of an antibiotic, see Antibiotics
amox	column name of an antibiotic, see Antibiotics
ampi	column name of an antibiotic, see Antibiotics
azit	column name of an antibiotic, see Antibiotics
aztr	column name of an antibiotic, see Antibiotics
cefa	column name of an antibiotic, see Antibiotics
cfra	column name of an antibiotic, see Antibiotics
cfep	column name of an antibiotic, see Antibiotics
cfot	column name of an antibiotic, see Antibiotics
cfox	column name of an antibiotic, see Antibiotics
cfta	column name of an antibiotic, see Antibiotics
cftr	column name of an antibiotic, see Antibiotics
cfur	column name of an antibiotic, see Antibiotics
chlo	column name of an antibiotic, see Antibiotics
cipr	column name of an antibiotic, see Antibiotics
clar	column name of an antibiotic, see Antibiotics
clin	column name of an antibiotic, see Antibiotics
clox	column name of an antibiotic, see Antibiotics
coli	column name of an antibiotic, see Antibiotics
czol	column name of an antibiotic, see Antibiotics
dapt	column name of an antibiotic, see Antibiotics
doxy	column name of an antibiotic, see Antibiotics
erta	column name of an antibiotic, see Antibiotics
eryt	column name of an antibiotic, see Antibiotics
fosf	column name of an antibiotic, see Antibiotics
fusi	column name of an antibiotic, see Antibiotics
gent	column name of an antibiotic, see Antibiotics
imip	column name of an antibiotic, see Antibiotics
kana	column name of an antibiotic, see Antibiotics
levo	column name of an antibiotic, see Antibiotics
linc	column name of an antibiotic, see Antibiotics
line	column name of an antibiotic, see Antibiotics
mero	column name of an antibiotic, see Antibiotics
metr	column name of an antibiotic, see Antibiotics
mino	column name of an antibiotic, see Antibiotics
moxi	column name of an antibiotic, see Antibiotics
nali	column name of an antibiotic, see Antibiotics
neom	column name of an antibiotic, see Antibiotics
neti	column name of an antibiotic, see Antibiotics
nitr	column name of an antibiotic, see Antibiotics
novo	column name of an antibiotic, see Antibiotics
norf	column name of an antibiotic, see Antibiotics
oflo	column name of an antibiotic, see Antibiotics
peni	column name of an antibiotic, see Antibiotics
pipe	column name of an antibiotic, see Antibiotics
pita	column name of an antibiotic, see Antibiotics
poly	column name of an antibiotic, see Antibiotics
qida	column name of an antibiotic, see Antibiotics
rifa	column name of an antibiotic, see Antibiotics
roxi	column name of an antibiotic, see Antibiotics
siso	column name of an antibiotic, see Antibiotics
teic	column name of an antibiotic, see Antibiotics
tetr	column name of an antibiotic, see Antibiotics
tica	column name of an antibiotic, see Antibiotics
tige	column name of an antibiotic, see Antibiotics
tobr	column name of an antibiotic, see Antibiotics
trim	column name of an antibiotic, see Antibiotics
trsu	column name of an antibiotic, see Antibiotics
vanc	column name of an antibiotic, see Antibiotics
...	parameters that are passed on to methods

Value

Ordered factor with levels Negative < Positive, unconfirmed < Positive.

Details

When country will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf).

Antibiotics

To define antibiotics column names, leave as it is to determine it automatically with guess_ab_col or input a text (case-insensitive) or use NULL to skip a column (e.g. tica = NULL). Non-existing columns will anyway be skipped with a warning.

Abbrevations of the column containing antibiotics in the form: abbreviation: generic name (ATC code)

amcl: amoxicillin+clavulanic acid (J01CR02), amik: amikacin (J01GB06), amox: amoxicillin (J01CA04), ampi: ampicillin (J01CA01), azit: azithromycin (J01FA10), azlo: azlocillin (J01CA09), aztr: aztreonam (J01DF01), cefa: cefaloridine (J01DB02), cfep: cefepime (J01DE01), cfot: cefotaxime (J01DD01), cfox: cefoxitin (J01DC01), cfra: cefradine (J01DB09), cfta: ceftazidime (J01DD02), cftr: ceftriaxone (J01DD04), cfur: cefuroxime (J01DC02), chlo: chloramphenicol (J01BA01), cipr: ciprofloxacin (J01MA02), clar: clarithromycin (J01FA09), clin: clindamycin (J01FF01), clox: flucloxacillin (J01CF05), coli: colistin (J01XB01), czol: cefazolin (J01DB04), dapt: daptomycin (J01XX09), doxy: doxycycline (J01AA02), erta: ertapenem (J01DH03), eryt: erythromycin (J01FA01), fosf: fosfomycin (J01XX01), fusi: fusidic acid (J01XC01), gent: gentamicin (J01GB03), imip: imipenem (J01DH51), kana: kanamycin (J01GB04), levo: levofloxacin (J01MA12), linc: lincomycin (J01FF02), line: linezolid (J01XX08), mero: meropenem (J01DH02), mezl: mezlocillin (J01CA10), mino: minocycline (J01AA08), moxi: moxifloxacin (J01MA14), nali: nalidixic acid (J01MB02), neom: neomycin (J01GB05), neti: netilmicin (J01GB07), nitr: nitrofurantoin (J01XE01), norf: norfloxacin (J01MA06), novo: novobiocin (an ATCvet code: QJ01XX95), oflo: ofloxacin (J01MA01), peni: (benzyl)penicillin (J01CE01), pipe: piperacillin (J01CA12), pita: piperacillin+tazobactam (J01CR05), poly: polymyxin B (J01XB02), pris: pristinamycin (J01FG01), qida: quinupristin/dalfopristin (J01FG02), rifa: rifampicin (J04AB02), roxi: roxithromycin (J01FA06), siso: sisomicin (J01GB08), teic: teicoplanin (J01XA02), tetr: tetracycline (J01AA07), tica: ticarcillin (J01CA13), tige: tigecycline (J01AA12), tobr: tobramycin (J01GB01), trim: trimethoprim (J01EA01), trsu: sulfamethoxazole and trimethoprim (J01EE01), vanc: vancomycin (J01XA01).

Examples

# NOT RUN {
library(dplyr)

septic_patients %>%
  mutate(EUCAST = mdro(.),
         BRMO = brmo(.))
# }