Implement EUCAST System for Antimicrobial Abbreviations

[Matthijs Berends]

See https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Disk_test_documents/Disk_abbreviations/EUCAST_system_for_antimicrobial_abbreviations.pdf for reference.

• Add the rules to column eucast in the antibiotics data set:

  1. Use the first three letters of the generic name
  2. Where this results in a clash, choose the next letter after the first two of the less commonly used agent that does not result in a clash; e.g CLArithromycin --> CLA, CLaVulanic acid --> CLV
  3. For combination agents, including beta-lactamase inhibitor combinations, use the first two letters of the first agent and the first letter of the second agent, using Rule 2 if necessary; e.g. AMoxicillin-Clavulanate --> AMC; TRimethoprim-Sulfamethoxazole -- > TRS; if a clash results, apply rule 2 e.g. TICarcillin -->TIC, TIcarcillin-cLavulanate -- > TIL
  4. Cephalosporins: Start with "C", remove the rest of the stem from the list below, and add the next two letters, using Rule 2 if necessary; e.g. CefaCLor --> CCL, CefTaroLine –>CTL
  5. Sulfonamides: Start with "S", remove the rest of the stem from the list below, and add the next two letters, using Rule 2 if necessary; e.g. SulfISoxazole --> SIS 6.

  Cephalosporin Stems		Sulphonamide Stems
  CEF	CEPH	SULF	SULPH
  CEFA	CEPHA	SULFA	SULPHA
  CEFO	CEPHO

• Build into as.ab()

• Return message or warning if an AB code matches both EUCAST and EARS-Net/WHONET (which will happen a lot...)

[Matthijs Berends]

This method is not reproducible for us: step II requires sorting and availability of the data. Furthermore, it is unknown what is meant with "the less commonly used agent".

It seems safer to just copy their table, which unfortunately only contains 123 agents, much less than the ~450 that are in the antibiotics data set.

[Matthijs Berends]

It's horrible, we're not complying with EUCAST regarding their methodologically unsound method to abbreviate antibiotics.

So these codes will not be added to the antibiotics data sets. Users can use the add_custom_antimicrobials() function to add own codes.