MIC (version 1.1.0)

qc_in_range: Check that MIC is within QC range

Description

Check whether MIC values are within acceptable range for quality control (QC). Every MIC experiment should include a control strain with a known MIC. The results of the experiment are only valid if the control strain MIC falls within the acceptable range. This function checks whether an MIC result is within the acceptable range given: 1) a control strain (usually identified as an ATCC or NCTC number), 2) an antibiotic name, and 3) a guideline (EUCAST or CLSI). The acceptable range is defined by 'QC_table', which is a dataset which is loaded with this package.

The source of the QC values is the WHONET QC Ranges and Targets available from the 'Antimicrobial Resistance Test Interpretation Engine' (AMRIE) repository: https://github.com/AClark-WHONET/AMRIE

Usage

qc_in_range(
  measurement,
  strain,
  ab,
  ignore_na = TRUE,
  guideline = "EUCAST",
  year = "2023"
)

Value

logical vector

Arguments

measurement

measured QC MIC

strain

control strain identifier (usually ATCC)

ab

antibiotic name (will be coerced to AMR::as.ab)

ignore_na

ignores NA (returns TRUE)

guideline

Guideline to use (EUCAST or CLSI)

year

Guideline year (version)

References

O’Brien TF, Stelling JM. WHONET: An Information System for Monitoring Antimicrobial Resistance. Emerg Infect Dis. 1995 Jun;1(2):66–66.

Examples

qc_in_range(AMR::as.mic(0.5), 25922, "GEN") == TRUE
qc_in_range(AMR::as.mic(8.0), 25922, "GEN") == FALSE