With the function mdro(), you can determine multi-drug resistant organisms (MDRO). It currently support these guidelines:

  • “Intrinsic Resistance and Exceptional Phenotypes Tables”, by EUCAST (European Committee on Antimicrobial Susceptibility Testing)
  • “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis”, by WHO (World Health Organization)
  • “WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)”, by RIVM (Rijksinstituut voor de Volksgezondheid, the Netherlands National Institute for Public Health and the Environment)

As an example, I will make a data set to determine multi-drug resistant TB:

Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:

The data set looks like this now:

We can now add the interpretation of MDR-TB to our data set:

And review the result with a frequency table:

freq(my_TB_data$mdr)

Frequency table of mdr from my_TB_data (5,000 x 8)

Class: factor > ordered (numeric)
Length: 5,000 (of which NA: 0 = 0.00%)
Levels: 5: Negative < Mono-resistance < Poly-resistance < Multidrug resistance…
Unique: 5

Item Count Percent Cum. Count Cum. Percent
1 Mono-resistance 3,206 64.1% 3,206 64.1%
2 Negative 689 13.8% 3,895 77.9%
3 Multidrug resistance 578 11.6% 4,473 89.5%
4 Poly-resistance 299 6.0% 4,772 95.4%
5 Extensive drug resistance 228 4.6% 5,000 100.0%