mdro.RdDetermine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
mdro(x, country = NULL, col_mo = NULL, info = TRUE, verbose = FALSE, ...) brmo(..., country = "nl") mrgn(x, country = "de", ...) eucast_exceptional_phenotypes(x, country = "EUCAST", ...)
| x | table with antibiotic columns, like e.g. |
|---|---|
| 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 |
| col_mo | column name of the unique 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 |
Ordered factor with levels Negative < Positive, unconfirmed < Positive.
When country will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (link).
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.
Available abbrevations of the column containing antibiotics in the form 'antimicrobial ID: name (ATC code)':
AMC: amoxicillin/clavulanic acid (J01CR02), AMK: amikacin (J01GB06), AMX: amoxicillin (J01CA04), AMP: ampicillin (J01CA01), AZM: azithromycin (J01FA10), AZL: azlocillin (J01CA09), ATM: aztreonam (J01DF01), RID: cefaloridine (J01DB02), 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), FLC: flucloxacillin (J01CF05), COL: colistin (J01XB01), CZO: cefazolin (J01DB04), DAP: daptomycin (J01XX09), DOX: doxycycline (J01AA02), ETP: ertapenem (J01DH03), ERY: erythromycin (J01FA01), FOS: fosfomycin (J01XX01), FUS: fusidic acid (J01XC01), GEN: gentamicin (J01GB03), IPM: imipenem (J01DH51), KAN: kanamycin (J01GB04), LVX: levofloxacin (J01MA12), LIN: lincomycin (J01FF02), LNZ: linezolid (J01XX08), MEM: meropenem (J01DH02), MEZ: mezlocillin (J01CA10), MNO: minocycline (J01AA08), MFX: moxifloxacin (J01MA14), MTR: metronidazole (J01XD01), 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), QDA: quinupristin/dalfopristin (J01FG02), RIF: rifampicin (J04AB02), 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 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.
# NOT RUN { library(dplyr) septic_patients %>% mutate(EUCAST = mdro(.), BRMO = brmo(.)) # }