Data Set with Clinical Breakpoints for SIR Interpretation

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:

For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.

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:

guideline
Name of the guideline
type
Breakpoint type, either "ECOFF", "animal", or "human"
host
Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"
method
Testing method, either "DISK" or "MIC"
site
Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
mo
Microbial ID, see as.mo()
rank_index
Taxonomic rank index of mo from 1 (subspecies/infraspecies) to 5 (unknown microorganism)
ab
Antimicrobial code as used by this package, EARS-Net and WHONET, see as.ab()
ref_tbl
Info about where the guideline rule can be found
disk_dose
Dose of the used disk diffusion method
breakpoint_S
Lowest MIC value or highest number of millimetres that leads to "S"
breakpoint_R
Highest MIC value or lowest number of millimetres that leads to "R", can be NA
uti
A logical value (TRUE/FALSE) to indicate whether the rule applies to a urinary tract infection (UTI)
is_SDD
A logical value (TRUE/FALSE) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 48 breakpoints.

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.

Examples

clinical_breakpoints
#> # A tibble: 40,217 × 14
#>    guideline   type  host  method site    mo            rank_index ab   ref_tbl 
#>    <chr>       <chr> <chr> <chr>  <chr>   <mo>               <dbl> <ab> <chr>   
#>  1 EUCAST 2025 human human DISK   NA      B_ACHRMB_XYLS          2 MEM  A. xylo…
#>  2 EUCAST 2025 human human MIC    NA      B_ACHRMB_XYLS          2 MEM  A. xylo…
#>  3 EUCAST 2025 human human DISK   NA      B_ACHRMB_XYLS          2 SXT  A. xylo…
#>  4 EUCAST 2025 human human MIC    NA      B_ACHRMB_XYLS          2 SXT  A. xylo…
#>  5 EUCAST 2025 human human DISK   NA      B_ACHRMB_XYLS          2 TZP  A. xylo…
#>  6 EUCAST 2025 human human MIC    NA      B_ACHRMB_XYLS          2 TZP  A. xylo…
#>  7 EUCAST 2025 human human DISK   NA      B_ACNTB                3 AMK  Acineto…
#>  8 EUCAST 2025 human human DISK   Uncomp… B_ACNTB                3 AMK  Acineto…
#>  9 EUCAST 2025 human human MIC    NA      B_ACNTB                3 AMK  Acineto…
#> 10 EUCAST 2025 human human MIC    Uncomp… B_ACNTB                3 AMK  Acineto…
#> # ℹ 40,207 more rows
#> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
#> #   uti <lgl>, is_SDD <lgl>

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