Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use as.rsi() to transform MICs or disks measurements to R/SI values.

rsi_translation

Format

A data.frame with 18,964 observations and 10 variables:

  • guideline
    Name of the guideline

  • method
    Either "MIC" or "DISK"

  • site
    Body site, e.g. "Oral" or "Respiratory"

  • mo
    Microbial ID, see as.mo()

  • ab
    Antibiotic ID, see as.ab()

  • ref_tbl
    Info about where the guideline rule can be found

  • disk_dose
    Dose of the used disk diffusion method

  • breakpoint_S
    Lowest MIC value or highest number of millimetres that leads to "S"

  • breakpoint_R
    Highest MIC value or lowest number of millimetres that leads to "R"

  • uti
    A logical value (TRUE/FALSE) to indicate whether the rule applies to a urinary tract infection (UTI)

Details

The repository of this AMR package contains a file comprising this exact data set: https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This file allows for machine reading EUCAST and CLSI guidelines, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.

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.