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SIRscan antibiotic code mapping

Source: R/data.R
sirscan_codes.Rd

Reference table mapping Bio-Rad SIRscan antibiotic codes to antibiotic names recognised by AMR::as.ab(). Used as the default lookup in import_sirscan_pheno() to translate codes that the AMR package does not recognise directly. Users can supply their own table via the sirscan_codes argument if their SIRscan configuration uses different code meanings.

Usage

sirscan_codes

Format

sirscan_codes A data frame with 11 rows and 2 columns:

Columns include:

  • sirscan_code: The antibiotic code as it appears in SIRscan export files.

  • ab_name: Antibiotic name string passed to AMR::as.ab() for translation.

Details

Confirmed codes (verified from Bio-Rad catalogue or collaborator communication): CF30 (cephalothin 30 mcg disk), MA (cefamandole), SSS (sulfonamides), SXT25 (trimethoprim/sulfamethoxazole 25 mcg disk).

Codes mapped by French CASFM/SIRscan convention, not yet confirmed in official Bio-Rad documentation: S (streptomycin), K (kanamycin), C (chloramphenicol), NALI (nalidixic acid), AZ (azithromycin), MM (minocycline), ERM (erythromycin).

Codes with no confirmed mapping (CAN, ECM, ICM) are absent from this table; they will return NA from AMR::as.ab() with a warning. Update this table or supply your own once the correct mappings are known.