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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. Currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022). Use as.sir() to transform MICs or disks measurements to SIR values.

Usage

clinical_breakpoints

Format

A tibble with 18,308 observations and 11 variables:

  • guideline
    Name of the guideline

  • method
    Either "DISK" or "MIC"

  • site
    Body site, 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
    Antibiotic ID, 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"

  • uti
    A logical value (TRUE/FALSE) to indicate whether the rule applies to a urinary tract infection (UTI)

Details

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.

See also

intrinsic_resistant

Examples

clinical_breakpoints
#> # A tibble: 18,308 × 11
#>    guideline method site  mo               rank_…¹ ab   ref_tbl  disk_…² break…³
#>    <chr>     <chr>  <chr> <mo>               <dbl> <ab> <chr>    <chr>     <dbl>
#>  1 EUCAST 2… MIC    NA    F_ASPRG_MGTS           2 AMB  Aspergi… NA            1
#>  2 EUCAST 2… MIC    NA    F_ASPRG_NIGR           2 AMB  Aspergi… NA            1
#>  3 EUCAST 2… MIC    NA    F_CANDD_ALBC           2 AMB  Candida  NA            1
#>  4 EUCAST 2… MIC    NA    F_CANDD_DBLN           2 AMB  Candida  NA            1
#>  5 EUCAST 2… MIC    NA    F_CANDD_GLBR           2 AMB  Candida  NA            1
#>  6 EUCAST 2… MIC    NA    F_CANDD_KRUS           2 AMB  Candida  NA            1
#>  7 EUCAST 2… MIC    NA    F_CANDD_PRPS           2 AMB  Candida  NA            1
#>  8 EUCAST 2… MIC    NA    F_CANDD_TRPC           2 AMB  Candida  NA            1
#>  9 EUCAST 2… MIC    NA    F_CRYPT_NFRM           2 AMB  Candida  NA            1
#> 10 EUCAST 2… DISK   NA    B_[ORD]_ENTRBCTR       5 AMC  Enterob… 20ug/1…      19
#> # … with 18,298 more rows, 2 more variables: breakpoint_R <dbl>, uti <lgl>, and
#> #   abbreviated variable names ¹​rank_index, ²​disk_dose, ³​breakpoint_S