Data Set with Bacterial Intrinsic Resistance

Source: R/data.R

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

Usage,
intrinsic_resistant

Format

A data.frame with 93,892 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/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' v3.2 (2020).

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.

Read more on Our Website!

On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.

Examples

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