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reference/clinical_breakpoints.md
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reference/clinical_breakpoints.md
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# Data Set with Clinical Breakpoints for SIR Interpretation
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Data set containing clinical breakpoints to interpret MIC and disk
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diffusion to SIR values, according to international guidelines. This
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dataset contain breakpoints for humans, 7 different animal groups, and
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ECOFFs.
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These breakpoints are currently implemented:
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- For **clinical microbiology**: EUCAST 2011-2025 and CLSI 2011-2025;
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- For **veterinary microbiology**: EUCAST 2021-2025 and CLSI 2019-2025;
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- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2025 and
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CLSI 2022-2025.
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Use [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) to transform
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MICs or disks measurements to SIR values.
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## Usage
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``` r
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clinical_breakpoints
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```
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## Format
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A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 40
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217 observations and 14 variables:
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- `guideline`
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Name of the guideline
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- `type`
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Breakpoint type, either "ECOFF", "animal", or "human"
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- `host`
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Host of infectious agent. This is mostly useful for veterinary
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breakpoints and is either "ECOFF", "aquatic", "cats", "cattle",
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"dogs", "horse", "human", "poultry", or "swine"
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- `method`
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Testing method, either "DISK" or "MIC"
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- `site`
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Body site for which the breakpoint must be applied, e.g. "Oral" or
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"Respiratory"
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- `mo`
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Microbial ID, see
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md)
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- `rank_index`
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Taxonomic rank index of `mo` from 1 (subspecies/infraspecies) to 5
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(unknown microorganism)
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- `ab`
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Antimicrobial code as used by this package, EARS-Net and WHONET, see
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[`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
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- `ref_tbl`
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Info about where the guideline rule can be found
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- `disk_dose`
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Dose of the used disk diffusion method
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- `breakpoint_S`
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Lowest MIC value or highest number of millimetres that leads to "S"
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- `breakpoint_R`
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Highest MIC value or lowest number of millimetres that leads to "R",
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can be `NA`
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- `uti`
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A [logical](https://rdrr.io/r/base/logical.html) value
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(`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary
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tract infection (UTI)
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- `is_SDD`
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A [logical](https://rdrr.io/r/base/logical.html) value
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(`TRUE`/`FALSE`) to indicate whether the intermediate range between
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"S" and "R" should be interpreted as "SDD", instead of "I". This
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currently applies to 48 breakpoints.
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## Details
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### Different Types of Breakpoints
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Supported types of breakpoints are ECOFF, animal, and human. ECOFF
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(Epidemiological cut-off) values are used in antimicrobial
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susceptibility testing to differentiate between wild-type and
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non-wild-type strains of bacteria or fungi.
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The default is `"human"`, which can also be set with the package option
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[`AMR_breakpoint_type`](https://amr-for-r.org/reference/AMR-options.md).
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Use
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[`as.sir(..., breakpoint_type = ...)`](https://amr-for-r.org/reference/as.sir.md)
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to interpret raw data using a specific breakpoint type, e.g.
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`as.sir(..., breakpoint_type = "ECOFF")` to use ECOFFs.
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### Imported From WHONET
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Clinical breakpoints in this package were validated through and imported
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from [WHONET](https://whonet.org), a free desktop Windows application
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developed and supported by the WHO Collaborating Centre for Surveillance
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of Antimicrobial Resistance. More can be read on [their
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website](https://whonet.org). The developers of WHONET and this `AMR`
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package have been in contact about sharing their work. We highly
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appreciate their great development on the WHONET software.
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Our import and reproduction script can be found here:
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<https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R>.
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### Response From CLSI and EUCAST
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The CEO of CLSI and the chairman of EUCAST have endorsed the work and
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public use of this `AMR` package (and consequently the use of their
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breakpoints) in June 2023, when future development of distributing
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clinical breakpoints was discussed in a meeting between CLSI, EUCAST,
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WHO, developers of WHONET software, and developers of this `AMR`
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package.
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### Download Note
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This `AMR` package (and the WHONET software as well) contains rather
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complex internal methods to apply the guidelines. For example, some
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breakpoints must be applied on certain species groups (which are in case
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of this package available through the
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[microorganisms.groups](https://amr-for-r.org/reference/microorganisms.groups.md)
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data set). It is important that this is considered when implementing the
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breakpoints for own use.
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## Download Our Reference Data
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All reference data sets in the AMR package - including information on
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microorganisms, antimicrobials, and clinical breakpoints - are freely
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available for download in multiple formats: R, MS Excel, Apache Feather,
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Apache Parquet, SPSS, and Stata.
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For maximum compatibility, we also provide machine-readable,
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tab-separated plain text files suitable for use in any software,
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including laboratory information systems.
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Visit [our website for direct download
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links](https://amr-for-r.org/articles/datasets.html), or explore the
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actual files in [our GitHub
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repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
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## See also
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[intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md)
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## Examples
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``` r
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clinical_breakpoints
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#> # A tibble: 40,217 × 14
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#> guideline type host method site mo rank_index ab ref_tbl
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#> <chr> <chr> <chr> <chr> <chr> <mo> <dbl> <ab> <chr>
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#> 1 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
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#> 2 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo…
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#> 3 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo…
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#> 4 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo…
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#> 5 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo…
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#> 6 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo…
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#> 7 EUCAST 2025 human human DISK NA B_ACNTB 3 AMK Acineto…
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#> 8 EUCAST 2025 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
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#> 9 EUCAST 2025 human human MIC NA B_ACNTB 3 AMK Acineto…
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#> 10 EUCAST 2025 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
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#> # ℹ 40,207 more rows
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#> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
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#> # uti <lgl>, is_SDD <lgl>
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```
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