# 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(x, guideline = NULL, col_mo = NULL, info = TRUE,
      verbose = FALSE, ...)

    brmo(x, guideline = "BRMO", ...)

    mrgn(x, guideline = "MRGN", ...)

    mdr_tb(x, guideline = "TB", ...)

    eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)

## Arguments

x | table with antibiotic columns, like e.g. `AMX` and `AMC`
guideline | a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.
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
verbose | print additional info: missing antibiotic columns per parameter
... | column name of an antibiotic, see section Antibiotics

## Source

EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (link)

World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (link)

Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (link)

## Value

For TB (`mdr_tb()`): Ordered factor with levels `Negative < Mono-resistance < Poly-resistance < Multidrug resistance < Extensive drug resistance`.

For everything else: Ordered factor with levels `Negative < Positive, unconfirmed < Positive`. The value `"Positive, unconfirmed"` means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests.

## Details

Currently supported guidelines are:

- `guideline = "EUCAST"`: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (link)

- `guideline = "TB"`: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (link)

- `guideline = "MRGN"`: (work in progress)

- `guideline = "BRMO"`: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (link)

Please suggest your own (country-specific) guidelines by letting us know: https://gitlab.com/msberends/AMR/issues/new.

## 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. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.

The following antibiotics are used for the functions `eucast_rules` and `mdro`. These are shown in the format 'antimicrobial ID: name (ATC code)', sorted by name:

AMK: amikacin (J01GB06), AMX: amoxicillin (J01CA04), AMC: amoxicillin/clavulanic acid (J01CR02), AMP: ampicillin (J01CA01), AZM: azithromycin (J01FA10), AZL: azlocillin (J01CA09), ATM: aztreonam (J01DF01), CAP: capreomycin (J04AB30), RID: cefaloridine (J01DB02), CZO: cefazolin (J01DB04), FEP: cefepime (J01DE01), CTX: cefotaxime (J01DD01), FOX: cefoxitin (J01DC01), CED: cefradine (J01DB09), CAZ: ceftazidime (J01DD02), CRO: ceftriaxone (J01DD04), CXM: cefuroxime (J01DC02), CHL: chloramphenicol (J01BA01), CIP: ciprofloxacin (J01MA02), CLR: clarithromycin (J01FA09), CLI: clindamycin (J01FF01), COL: colistin (J01XB01), DAP: daptomycin (J01XX09), DOX: doxycycline (J01AA02), ETP: ertapenem (J01DH03), ERY: erythromycin (J01FA01), ETH: ethambutol (J04AK02), FLC: flucloxacillin (J01CF05), FOS: fosfomycin (J01XX01), FUS: fusidic acid (J01XC01), GAT: gatifloxacin (J01MA16), GEN: gentamicin (J01GB03), IPM: imipenem (J01DH51), INH: isoniazid (J04AC01), KAN: kanamycin (J01GB04), LVX: levofloxacin (J01MA12), LIN: lincomycin (J01FF02), LNZ: linezolid (J01XX08), MEM: meropenem (J01DH02), MTR: metronidazole (J01XD01), MEZ: mezlocillin (J01CA10), MNO: minocycline (J01AA08), MFX: moxifloxacin (J01MA14), NAL: nalidixic acid (J01MB02), NEO: neomycin (J01GB05), NET: netilmicin (J01GB07), NIT: nitrofurantoin (J01XE01), NOR: norfloxacin (J01MA06), NOV: novobiocin (an ATCvet code: QJ01XX95), OFX: ofloxacin (J01MA01), OXA: oxacillin (J01CF04), PEN: penicillin G (J01CE01), PIP: piperacillin (J01CA12), TZP: piperacillin/tazobactam (J01CR05), PLB: polymyxin B (J01XB02), PRI: pristinamycin (J01FG01), PZA: pyrazinamide (J04AK01), QDA: quinupristin/dalfopristin (J01FG02), RIB: rifabutin (J04AB04), RIF: rifampicin (J04AB02), RIF: rifampin (J04AB02), RFP: rifapentine (J04AB05), RXT: roxithromycin (J01FA06), SIS: sisomicin (J01GB08), TEC: teicoplanin (J01XA02), TCY: tetracycline (J01AA07), TIC: ticarcillin (J01CA13), TGC: tigecycline (J01AA12), TOB: tobramycin (J01GB01), TMP: trimethoprim (J01EA01), SXT: trimethoprim/sulfamethoxazole (J01EE01), VAN: vancomycin (J01XA01).

## Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a 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(.))
    # }