# Determine multidrug-resistant organisms (MDRO) — mdro • AMR (for R)
Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.

# Determine multidrug-resistant organisms (MDRO)

`mdro.Rd`

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

    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` 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: penicillin (J01RA01), 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 omprehensive tutorial about how to conduct AMR analysis and find the complete documentation of all functions, which reads a lot easier than in R.

## Examples

    # NOT RUN {
    library(dplyr)

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