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(.))
# }