Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
intrinsic_resistant
A data.frame with 49,462 observations and 2 variables:
microorganism
Name of the microorganism
antibiotic
Name of the antibiotic drug
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.
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.
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!
if (require("dplyr")) { intrinsic_resistant %>% filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>% pull(microorganism) # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" }