Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.

mdro(x, guideline = NULL, col_mo = NULL, info = TRUE,
  verbose = FALSE, pct_required_classes = 0.5, ...)

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

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

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

mdr_cmi2012(x, guideline = "CMI2012", ...)

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

Arguments

x

data with antibiotic columns, like e.g. AMX and AMC

guideline

a specific guideline to follow. When left empty, the publication by Magiorakos et al. (2012, Clinical Microbiology and Infection) will be followed, see Details.

col_mo

column name of the IDs of the microorganisms (see as.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

pct_required_classes

minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for S. aureus. Setting this pct_required_classes argument to 0.5 (default) means that for every S. aureus isolate at least 8 different classes must be available. Any lower number of available classes will return NA for that isolate.

...

column name of an antibiotic, see section Antibiotics

verbose

a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.

Source

Please see Details for the list of publications used for this function.

Value

  • CMI 2012 paper - function mdr_cmi2012() or mdro():
    Ordered factor with levels Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR)

  • TB guideline - function mdr_tb() or mdro(..., guideline = "TB"):
    Ordered factor with levels Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively 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

Details

For the pct_required_classes argument, values above 1 will be divided by 100. This is to support both fractions (0.75 or 3/4) and percentages (75). Currently supported guidelines are (case-insensitive):

  • guideline = "CMI2012": Magiorakos AP, Srinivasan A et al. "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (link)

  • 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.

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 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), SAM: ampicillin/sulbactam (J01CR01), AZM: azithromycin (J01FA10), AZL: azlocillin (J01CA09), ATM: aztreonam (J01DF01), CAP: capreomycin (J04AB30), RID: cefaloridine (J01DB02), CZO: cefazolin (J01DB04), FEP: cefepime (J01DE01), CTX: cefotaxime (J01DD01), CTT: cefotetan (J01DC05), FOX: cefoxitin (J01DC01), CPT: ceftaroline (J01DI02), CAZ: ceftazidime (J01DD02), CRO: ceftriaxone (J01DD04), CXM: cefuroxime (J01DC02), CED: cephradine (J01DB09), CHL: chloramphenicol (J01BA01), CIP: ciprofloxacin (J01MA02), CLR: clarithromycin (J01FA09), CLI: clindamycin (J01FF01), COL: colistin (J01XB01), DAP: daptomycin (J01XX09), DOR: doripenem (J01DH04), 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), GEH: gentamicin-high (no ATC code), 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 (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), RFP: rifapentine (J04AB05), RXT: roxithromycin (J01FA06), SIS: sisomicin (J01GB08), STH: streptomycin-high (no ATC code), TEC: teicoplanin (J01XA02), TLV: telavancin (J01XA03), TCY: tetracycline (J01AA07), TIC: ticarcillin (J01CA13), TCC: ticarcillin/clavulanic acid (J01CR03), 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

library(dplyr)

example_isolates %>%
  mdro() %>%
  freq()

# \donttest{
example_isolates %>%
  mutate(EUCAST = eucast_exceptional_phenotypes(.),
         BRMO = brmo(.),
         MRGN = mrgn(.))

example_isolates %>%
  rename(PIP = TZP) %>% # no piperacillin, so take piperacillin/tazobactam
  mrgn() %>%            # check German guideline
  freq()                # check frequencies
# }