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WHONET agent codes SUD and ROX resolve to the wrong antimicrobials in clinical_breakpoints #308

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@msberends

In the WHONET-based import of clinical breakpoints (data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R), agents are coded with as.ab(WHONET_ABX_CODE). For two WHONET codes this resolves to a different agent than the one WHONET means:

WHONET code WHONET agent Currently coded as Rows in clinical_breakpoints
SUD Sulbactam-durlobactam SUD (Sulfadimethoxine) 6 (CLSI 2024-2026, Acinetobacter, MIC 4/16, disk 10/10 µg 17/13)
ROX not named in WHONET's Antibiotics.txt CXM (Cefuroxime) 2 (EUCAST 2011, M. catarrhalis MIC 0.5/2, H. influenzae MIC 1/32)
  • SUD: the values are unmistakably sulbactam-durlobactam (Xacduro), so these breakpoints are now interpreted for sulfadimethoxine. Sulbactam-durlobactam is not in antimicrobials yet (as.ab("Sulbactam-durlobactam") returns CTS, cefotaxime/sulbactam). It needs to be added to antimicrobials, after which the import can map SUD to it.
  • ROX: ROX conventionally means roxithromycin (RXT in this package), yet it is coded as cefuroxime. This needs verification against the EUCAST 2011 tables before deciding the correct code.

Also related: WHONET STR (streptomycin) resolves to STR (streptoduocin) instead of STR1 (streptomycin), affecting 128 rows across CLSI and EUCAST 2011-2026.

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