Classify MDR and XDR — prep_classify_mdr_xdr • anumaan

Classifies isolates as MDR (Multidrug Resistant) and XDR (Extensively Drug Resistant) in a single pass using Magiorakos 2012 criteria.

Usage

prep_classify_mdr_xdr(
  data,
  definition = "Magiorakos",
  organism_group_col = "org_group"
)

Arguments

data: Data frame with class-level resistance data.
definition: Character. Classification criteria. Default "Magiorakos".
organism_group_col: Character. Organism group column for pathogen-specific thresholds. Default "org_group".

Value

Data frame with mdr, mdr_confidence, mdr_method, n_resistant_categories, resistant_categories, xdr, xdr_confidence, and xdr_method columns added.

Details

MDR: resistant to at least one agent in three or more antimicrobial categories. XDR: susceptible to at most two antimicrobial categories.

Requires class_result_event column (run prep_collapse_class_level() first, then rename class_resistance to class_result_event).

References

Magiorakos AP et al. Clin Microbiol Infect. 2012;18(3):268-281.