mdro.RdDetermine 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", ...)
| x | table with antibiotic columns, like e.g. |
|---|---|
| guideline | a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details. |
| col_mo | column name of the IDs of the microorganisms (see |
| info | print progress |
| verbose | print additional info: missing antibiotic columns per parameter |
| ... | column name of an antibiotic, see section Antibiotics |
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)
TB guideline - function mdr_tb() or mdro(..., guideline = "TB"):
Ordered factor with levels Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensive drug-resistant
German guideline - function mrgn() or mdro(..., guideline = "MRGN"):
Ordered factor with levels Negative < 3MRGN < 4MRGN
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
Currently supported guidelines are (case-insensitive):
guideline = "EUCAST": The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (link)
guideline = "TB": The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (link)
guideline = "MRGN": The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6
guideline = "BRMO": The Dutch national guideline - 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.
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 below 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).
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.
library(dplyr) example_isolates %>% mutate(EUCAST = mdro(.), BRMO = brmo(.), MRGN = mrgn(.)) example_isolates %>% rename(PIP = TZP) %>% # no piperacillin, so take piperacillin/tazobactam mrgn() %>% # check German guideline freq() # check frequencies