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Import and process antimicrobial susceptibility data from SIRscan (Bio-Rad)

Source: R/import_pheno.R
import_sirscan_pheno.Rd

SIRscan (Bio-Rad) exports AST results as three separate semicolon-delimited CSV files: MIC values (CMI), disk diffusion diameters (DIAM), and SIR interpretations (INTERPR). Each file shares the same row structure (one row per isolate) and antibiotic columns. This function reads one or more of these files, pivots to long format, and returns a standardised AMRgen data frame.

Usage

import_sirscan_pheno(
  mic_file = NULL,
  disk_file = NULL,
  interpr_file = NULL,
  source = NULL,
  species = NULL,
  ab = NULL,
  instrument_guideline = NULL,
  sirscan_codes = sirscan_codes,
  interpret_eucast = FALSE,
  interpret_clsi = FALSE,
  interpret_ecoff = FALSE
)

Arguments

mic_file

Path to the SIRscan CMI (MIC) export file. Optional.

disk_file

Path to the SIRscan DIAM (disk diffusion) export file. Optional.

interpr_file

Path to the SIRscan INTERPR (SIR interpretation) export file. Optional. At least one of mic_file, disk_file, or interpr_file must be supplied.

source

Optional source label for the source output column.

species

Optional fixed species string applied to all rows (parsed via AMR::as.mo()). If NULL, the Germe column from the file is used.

ab

Optional antibiotic filter/override passed to interpret_pheno().

instrument_guideline

Optional guideline string for the guideline column (e.g. "EUCAST 2023").

sirscan_codes

A data frame mapping SIRscan antibiotic codes (sirscan_code) to antibiotic names (ab_name) recognised by AMR::as.ab(). Defaults to the built-in sirscan_codes table. Supply your own data frame to override mappings — for example if your SIRscan configuration uses S, K, or C for different agents than the defaults. Set to NULL to skip the lookup and pass all codes directly to AMR::as.ab().

interpret_eucast

Interpret MIC/disk values against EUCAST human breakpoints (default FALSE).

interpret_clsi

Interpret MIC/disk values against CLSI human breakpoints (default FALSE).

interpret_ecoff

Interpret MIC/disk values against ECOFF values (default FALSE).

Value

A standardised long-format data frame with columns: id, drug, mic, disk, pheno_provided, pheno_eucast, pheno_clsi, ecoff, method, platform, guideline, source, spp_pheno, collection_date, specimen_type.

Details

Files have a 4-row metadata header (institution, lab, export date, period) followed by a semicolon-delimited data block. Latin-1 (Windows-1252) encoding is assumed, as is standard for French-locale SIRscan exports.

Examples

if (FALSE) { # \dontrun{
# Import all three SIRscan export files
pheno <- import_sirscan_pheno(
  mic_file     = "CMI_SALMO.csv",
  disk_file    = "DIAM_SALMO.csv",
  interpr_file = "INTERPR_SALMO.csv"
)

# MIC + interpretations only, with EUCAST re-interpretation
pheno <- import_sirscan_pheno(
  mic_file = "CMI_SALMO.csv",
  interpr_file = "INTERPR_SALMO.csv",
  species = "Salmonella enterica",
  interpret_eucast = TRUE
)
} # }