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 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
Use as.sir() to transform MICs or disks measurements to SIR values.
Format
A tibble with 34 063 observations and 14 variables:
guideline
Name of the guidelinetype
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, seeas.mo()rank_index
Taxonomic rank index ofmofrom 1 (subspecies/infraspecies) to 5 (unknown microorganism)ab
Antibiotic code as used by this package, EARS-Net and WHONET, seeas.ab()ref_tbl
Info about where the guideline rule can be founddisk_dose
Dose of the used disk diffusion methodbreakpoint_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"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 24 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.
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
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository. They allow for machine reading EUCAST and CLSI guidelines, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI, though initiatives have started to overcome these burdens.
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 using the breakpoints for own use.
Examples
clinical_breakpoints
#> # A tibble: 34,063 × 14
#> guideline type host method site mo rank_index ab ref_tbl
#> <chr> <chr> <chr> <chr> <chr> <mo> <dbl> <ab> <chr>
#> 1 EUCAST 2024 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 2 EUCAST 2024 human human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 3 EUCAST 2024 human human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 4 EUCAST 2024 human human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 5 EUCAST 2024 human human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 6 EUCAST 2024 human human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 7 EUCAST 2024 human human DISK NA B_ACNTB 3 AMK Acineto…
#> 8 EUCAST 2024 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
#> 9 EUCAST 2024 human human MIC NA B_ACNTB 3 AMK Acineto…
#> 10 EUCAST 2024 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
#> # ℹ 34,053 more rows
#> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
#> # uti <lgl>, is_SDD <lgl>