MIC (version 1.1.0)

standardise_mic: Standardise MIC to control strain

Description

MIC experiments are generally quality-controlled by including a control strain with a known MIC. The MIC result for the control strain should be a particular target MIC, or at least within an acceptable range. This function standardises a measured MIC to the target MIC 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 definition of standardisation in this context is to adjust the measured MIC based on the QC MIC. This is based on the following principles and assumption:

1. A measured MIC is composed of two components: the true MIC and a measurement error. The measurement error is considered to be inevitable when measuring MICs, and is likely to be further composed of variability in laboratory conditions and operator interpretation.

2. It is assumed that the MIC of the control strain in the experiment has also been affected by this error.

The standardisation applied by this function uses the measured QC strain MIC as a reference point, and scales the rest of the MICs to this reference. In general, this means that the MICs are doubled or halved, depending on the result of the QC MIC. A worked example is provided below and illustrates the transformation that this function applies.

There is no current evidence base for this approach, therefore, this function is considered experimental and should be used with caution.

Usage

standardise_mic(
  test_measurement,
  qc_measurement,
  strain,
  ab,
  prefer_upper = FALSE,
  ignore_na = TRUE,
  guideline = "EUCAST",
  year = "2023",
  force = TRUE
)

Value

AMR::mic vector

Arguments

test_measurement

Measured MIC to standardise

qc_measurement

Measured QC MIC to standardise to

strain

control strain identifier (usually ATCC)

ab

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

prefer_upper

Where the target MIC is a range, prefer the upper value in the range

ignore_na

Ignore NA (returns AMR::NA_mic_)

guideline

Guideline to use (EUCAST or CLSI)

year

Guideline year (version)

force

Force into MIC-compatible format after standardisation

Examples

# Ref strain QC MIC for GEN is 0.5
standardise_mic(
  test_measurement = c(AMR::as.mic(">8.0"),  # QC = 1, censored MIC remains censored
                       AMR::as.mic(4.0),  # QC = 0.5 which is on target, so stays same
                       AMR::as.mic(2),  # QC = 1, so scaled down to 1
                       AMR::as.mic(2)),  # QC = 0.25, so scaled up to 8
  qc_measurement = c(AMR::as.mic(1),
                     AMR::as.mic(0.5),
                     AMR::as.mic(1),
                     AMR::as.mic(0.25)),
  strain = 25922,
  ab = AMR::as.ab("GEN"))