clinical_breakpoints {AMR}R Documentation

Data Set with Clinical Breakpoints for SIR Interpretation

Description

Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.

These breakpoints are currently implemented:

Use as.sir() to transform MICs or disks measurements to SIR values.

Usage

clinical_breakpoints

Format

A tibble with 40 217 observations and 14 variables:

Details

Different Types of Breakpoints

Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.

The default is "human", which can also be set with the package option AMR_breakpoint_type. Use as.sir(..., breakpoint_type = ...) to interpret raw data using a specific breakpoint type, e.g. as.sir(..., breakpoint_type = "ECOFF") to use ECOFFs.

Imported From WHONET

Clinical breakpoints in this package were validated through and imported from WHONET, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on their website. The developers of WHONET and this AMR package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.

Our import and reproduction script can be found here: https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R.

Response From CLSI and EUCAST

The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this AMR package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, WHO, developers of WHONET software, and developers of this AMR package.

Download Note

This AMR package (and the WHONET software as well) contains rather complex internal methods to apply the guidelines. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the microorganisms.groups data set). It is important that this is considered when implementing the breakpoints for own use.

Download Our Reference Data

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit our website for direct download links, or explore the actual files in our GitHub repository.

See Also

intrinsic_resistant

Examples

clinical_breakpoints

[Package AMR version 3.0.0 Index]