AMR: intrinsic_resistant – R documentation

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AMR

intrinsic_resistant

Data Set with Bacterial Intrinsic Resistance

Description

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/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' 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.

Examples

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

AMR

Antimicrobial Resistance Data Analysis

v1.6.0

GPL-2 | file LICENSE

Authors

Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>), Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>), Alexander W. Friedrich [aut, ths] (<https://orcid.org/0000-0003-4881-038X>), Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>), Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>), Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>), Judith M. Fonville [ctb], Erwin E. A. Hassing [ctb], Eric H. L. C. M. Hazenberg [ctb], Gwen Knight [ctb], Annick Lenglet [ctb], Bart C. Meijer [ctb], Sofia Ny [ctb], Rogier P. Schade [ctb], Dennis Souverein [ctb], Anthony Underwood [ctb]

Initial release

2021-03-14