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Import and process antimicrobial phenotype data exported from Vitek instruments

Source: R/import_pheno.R
import_vitek_pheno.Rd

This function imports antimicrobial susceptibility testing (AST) data from Vitek instrument output files (wide CSV format) and converts it to the standardised long-format used by AMRgen.

Usage

import_vitek_pheno(
  input,
  sample_col = "Lab ID",
  source = NULL,
  species = NULL,
  ab = NULL,
  instrument_guideline = NULL,
  use_expertized = TRUE,
  interpret_eucast = FALSE,
  interpret_clsi = FALSE,
  interpret_ecoff = FALSE,
  include_dates = TRUE
)

Arguments

input

A dataframe or path to a CSV file containing Vitek AST output data

sample_col

String indicating the name of the column containing sample identifiers. Default: "Lab ID"

source

Optional string value to record in the source column for all data points (e.g., dataset name or study identifier)

species

Optional string indicating a single species to use for phenotype interpretation (otherwise this is inferred per-sample from the input)

ab

Optional string indicating a single antibiotic to use for phenotype interpretation (otherwise this is inferred per-sample from the input)

instrument_guideline

Optional string indicating the guideline used by the instrument for SIR interpretation (e.g., "EUCAST 2025", "CLSI 2025"), used to record the guideline in the output file. Default: NULL

use_expertized

Use expertized SIR (TRUE, default) or instrument SIR (FALSE)

interpret_eucast

A logical value (default is FALSE). If TRUE, the function will re-interpret the susceptibility phenotype (SIR) for each observation based on the MIC values, against EUCAST human breakpoints. These will be reported in a new column pheno_eucast, of class sir.

interpret_clsi

A logical value (default is FALSE). If TRUE, the function will re-interpret the susceptibility phenotype (SIR) for each observation based on the MIC values, against CLSI human breakpoints. These will be reported in a new column pheno_clsi, of class sir.

interpret_ecoff

A logical value (default is FALSE). If TRUE, the function will re-interpret the wildtype vs nonwildtype status for each observation based on the MIC values, against epidemiological cut-off (ECOFF) values. These will be reported in a new column ecoff, of class sir and coded as NWT (nonwildtype) or WT (wildtype).

include_dates

Logical indicating whether to include collection_date and testing_date in output. Default: TRUE

Value

Standardised AST data frame