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.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2023 and CLSI 2011-2023.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2023 and CLSI 2019-2023.
Use as.sir() to transform MICs or disks measurements to SIR values.
Format
A tibble with 29 883 observations and 13 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)
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 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, the WHO, and developers of WHONET and the 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, SAS, 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 internal methods to apply the guidelines, which is rather complex. 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: 29,883 × 13
#> guideline type host method site mo rank_index ab ref_tbl
#> <chr> <chr> <chr> <chr> <chr> <mo> <dbl> <ab> <chr>
#> 1 EUCAST 2023 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 2 EUCAST 2023 human human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 3 EUCAST 2023 human human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 4 EUCAST 2023 human human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 5 EUCAST 2023 human human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 6 EUCAST 2023 human human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 7 EUCAST 2023 human human DISK NA B_ACNTB 3 AMK Acineto…
#> 8 EUCAST 2023 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
#> 9 EUCAST 2023 human human MIC NA B_ACNTB 3 AMK Acineto…
#> 10 EUCAST 2023 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
#> # ℹ 29,873 more rows
#> # ℹ 4 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
#> # uti <lgl>