Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This data set contains breakpoints for humans, 7 different animal groups, and ECOFFs.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2026 and CLSI 2011-2026;
For veterinary microbiology: EUCAST 2021-2026 and CLSI 2019-2026;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.
Use as.sir() to transform MICs or disks measurements to SIR values.
Format
A tibble with 60 173 observations and 15 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 7 (non-species related breakpoints), used to choose the most specific breakpoint; blocking rows (see Details) have the rank index of their organism + 0.1ab
Antimicrobial 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", isNAfor blocking rows (see Details)breakpoint_R
Highest MIC value or lowest number of millimetres that leads to "R", can beNAuti
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 72 breakpoints.note
Notes from the guideline that apply to the breakpoint, if available
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.
Blocking Rows
Where EUCAST lists an organism but gives no breakpoint for it (e.g. "IE", "-", "Note", breakpoints in brackets, or an organism excluded with "except"), as.sir() must not fall back to the breakpoint of a broader taxon, such as the breakpoint for Vibrio spp. where EUCAST gives "IE" for V. fluvialis. Such cases are included as "blocking rows": rows in which breakpoint_S and breakpoint_R are both NA and the note starts with "[No breakpoint]" followed by the reason. as.sir() returns NA for these. This currently applies to 14 523 rows. Remove them with subset(clinical_breakpoints, !is.na(breakpoint_S)) if only actual breakpoints are needed.
Imported From WHONET
Some 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.
From WHONET, imported were:
All CLSI breakpoints, including ECOFF
All non-human EUCAST breakpoints, including ECOFF
Human EUCAST breakpoints between 2011 and 2018
Human EUCAST antifungal breakpoints between 2019 and 2025
Human EUCAST breakpoints from 2019 onwards (antifungal breakpoints from 2026 onwards) were retrieved directly from the EUCAST Clinical Breakpoint Tables published on https://www.eucast.org, using this script.
Our WHONET import script can be found here.
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: 60,173 × 15
#> guideline type host method site mo rank_index ab ref_tbl
#> <chr> <chr> <chr> <chr> <chr> <mo> <dbl> <ab> <chr>
#> 1 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2.1 FDC A.xylosox…
#> 2 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2.1 FDC A.xylosox…
#> 3 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 MEM A.xylosox…
#> 4 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 MEM A.xylosox…
#> 5 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 SXT A.xylosox…
#> 6 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 SXT A.xylosox…
#> 7 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 TZP A.xylosox…
#> 8 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 TZP A.xylosox…
#> 9 EUCAST 2026 human human DISK NA B_ACNTB 3.1 AMC Acinetoba…
#> 10 EUCAST 2026 human human MIC NA B_ACNTB 3.1 AMC Acinetoba…
#> # ℹ 60,163 more rows
#> # ℹ 6 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
#> # uti <lgl>, is_SDD <lgl>, note <chr>