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.
In the WHONET-based import of clinical breakpoints (
data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R), agents are coded withas.ab(WHONET_ABX_CODE). For two WHONET codes this resolves to a different agent than the one WHONET means:clinical_breakpointsSUDSUD(Sulfadimethoxine)ROXAntibiotics.txtCXM(Cefuroxime)antimicrobialsyet (as.ab("Sulbactam-durlobactam")returnsCTS, cefotaxime/sulbactam). It needs to be added toantimicrobials, after which the import can mapSUDto it.ROXconventionally means roxithromycin (RXTin 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 toSTR(streptoduocin) instead ofSTR1(streptomycin), affecting 128 rows across CLSI and EUCAST 2011-2026.