AMR/reference/intrinsic_resistant.md

Data Set Denoting Bacterial Intrinsic Resistance

Data set containing 'EUCAST Expected Resistant Phenotypes' of all bug-drug combinations between the microorganisms and antimicrobials data sets.

Usage

intrinsic_resistant

Format

A tibble with 294 079 observations and 3 variables:

• mo
  Microorganism ID which occurs in microorganisms$mo. Names can be retrieved using mo_name().

• ab
  Antimicrobial ID which occurs in antimicrobials$ab. Names can be retrieved using ab_name().

• version
  Guideline name and version.

Details

This data set is currently strictly follows 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). The

This data set is internally used by:

• not_intrinsic_resistant() (an antimicrobial selector)

• mo_is_intrinsic_resistant()

• wisca() to model \\beta(1, 9999)\ for resistant bug-drug combinations, per doi:10.1093/jac/dkv397

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

intrinsic_resistant
#> # A tibble: 294,079 × 3
#>    mo          ab   version                                    
#>    <mo>        <ab> <chr>                                      
#>  1 B_GRAMP     ATM  'EUCAST Expected Resistant Phenotypes' v1.2
#>  2 B_GRAMP     COL  'EUCAST Expected Resistant Phenotypes' v1.2
#>  3 B_GRAMP     NAL  'EUCAST Expected Resistant Phenotypes' v1.2
#>  4 B_GRAMP     PLB  'EUCAST Expected Resistant Phenotypes' v1.2
#>  5 B_GRAMP     TEM  'EUCAST Expected Resistant Phenotypes' v1.2
#>  6 B_ANAER-POS ATM  'EUCAST Expected Resistant Phenotypes' v1.2
#>  7 B_ANAER-POS COL  'EUCAST Expected Resistant Phenotypes' v1.2
#>  8 B_ANAER-POS NAL  'EUCAST Expected Resistant Phenotypes' v1.2
#>  9 B_ANAER-POS PLB  'EUCAST Expected Resistant Phenotypes' v1.2
#> 10 B_ANAER-POS TEM  'EUCAST Expected Resistant Phenotypes' v1.2
#> # ℹ 294,069 more rows