Data set with bacterial intrinsic resistance

Source: R/data.R

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

intrinsic_resistant

Format

A data.frame with 49,462 observations and 2 variables:

  • microorganism
    Name of the microorganism

  • antibiotic
    Name of the antibiotic drug

Details

The repository of this AMR package contains a file comprising this exact data set: https://github.com/msberends/AMR/blob/master/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, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.

Read more on our website!

On our website https://msberends.github.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!

Examples

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