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(), verbose = FALSE)

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
verbose

print additional info: missing antibiotic columns per parameter
...

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" (link).

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).

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

Examples

# NOT RUN {
library(dplyr)

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