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# Data Set with Clinical Breakpoints for SIR Interpretation

Source: `R/data.R`
`clinical_breakpoints.Rd`

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.

## Usage

    clinical_breakpoints

## Format

A tibble with 45 735 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 72 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.

## See also

intrinsic_resistant

## Examples

    clinical_breakpoints
    #> # A tibble: 45,735 × 14
    #>    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 MEM  A. xylo…
    #>  2 EUCAST 2026 human human MIC    NA      B_ACHRMB_XYLS          2 MEM  A. xylo…
    #>  3 EUCAST 2026 human human DISK   NA      B_ACHRMB_XYLS          2 SXT  A. xylo…
    #>  4 EUCAST 2026 human human MIC    NA      B_ACHRMB_XYLS          2 SXT  A. xylo…
    #>  5 EUCAST 2026 human human DISK   NA      B_ACHRMB_XYLS          2 TZP  A. xylo…
    #>  6 EUCAST 2026 human human MIC    NA      B_ACHRMB_XYLS          2 TZP  A. xylo…
    #>  7 EUCAST 2026 human human DISK   NA      B_ACNTB                3 AMK  Acineto…
    #>  8 EUCAST 2026 human human DISK   Uncomp… B_ACNTB                3 AMK  Acineto…
    #>  9 EUCAST 2026 human human MIC    NA      B_ACNTB                3 AMK  Acineto…
    #> 10 EUCAST 2026 human human MIC    Uncomp… B_ACNTB                3 AMK  Acineto…
    #> # ℹ 45,725 more rows
    #> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
    #> #   uti <lgl>, is_SDD <lgl>