Data Set with Bacterial Intrinsic Resistance

Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.

Usage,

intrinsic_resistant

Format

A data.frame with 134,956 observations and 2 variables:

mo
Microorganism ID
ab
Antibiotic ID

Details

The repository of this AMR package contains a file comprising this data set with full taxonomic and antibiotic names: https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt. This file allows for machine reading EUCAST guidelines about intrinsic resistance, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.

This data set is based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021).

Reference Data Publicly Available

All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.

Examples

subset(intrinsic_resistant,
       antibiotic == "Vancomycin" & microorganism %like% "Enterococcus")$microorganism
#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"

# \donttest{
if (require("dplyr")) {
  intrinsic_resistant %>%
    filter(antibiotic == "Vancomycin" & microorganism %like% "Enterococcus") %>% 
    pull(microorganism)
  #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
}
# }

Format

Details

Reference Data Publicly Available

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Examples