qc_on_target: Check that QC measurement is at the required target...

In MIC: Analysis of Antimicrobial Minimum Inhibitory Concentration Data

Check that QC measurement is at the required target

Description

MIC experiments should include a control strain with a known MIC. The MIC result for the control strain should be a particular target MIC. This function checks whether the target MIC was achieved given: 1) a control strain (usually identified as an ATCC or NCTC number), 2) an antibiotic name, and 3) a guideline (EUCAST or CLSI).

Since QC target values are currently not publicly available in an easy to use format, this function takes a pragmatic approach – for most antibiotics and QC strains, the target is assumed to be the midpoint of the acceptable range. This approximation is not necessarily equal to the QC target reported by guideline setting bodies such as EUCAST. Therefore, this function is considered experimental and should be used with caution.

This function can be used alongnside qc_in_range(), which checks whether the MIC is within the acceptable range.

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

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)

Value

logical vector

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_on_target(AMR::as.mic(0.5), 25922, "GEN") == TRUE

MIC documentation built on April 12, 2025, 2:26 a.m.