Fig. 4: Performance of abritAMR pipeline to detect AMR mechanisms compared to PCR.

Each panel details the identification of AMR mechanisms by abritAMR compared to the ‘gold standard’ multiplex PCR assays used in our laboratory. True positive, detected by both PCR and abritAMR; true negative, not detected by either PCR or abritAMR; false positive, detected by abritAMR but not multiplex PCR, and within the known range of the PCR assay; false negative, detected by multiplex PCR but not by abritAMR. Panel A, mec genes compared to multiplex PCR (mecA/mecC, no mecC detected by either method). Panel B, van genes compared to multiplex PCR (vanA/B/C). Panel C1, detection of genes within carbapenemase and ESBL gene families compared to multiplex PCR panel (AusDiagnostics CRE panel); asterisks represent groups where discrepancies were identified, and expanded out in Panel C2 to show the specific gene discrepancies between the two methods. Abbreviations: AMR antimicrobial resistance, PCR polymerase chain reaction, CP carbapenemase, ESBL extended-spectrum beta-lactamase. Source data are provided as a Source Data file.