Aims Carbapenem resistance in Bacteroides fragilis is emerging and is mainly attributed to insertion sequence (IS)-mediated activation of the carbapenemase gene cfiA. We investigated the use of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and the CarbaNP assay for the rapid identification of these strains.
Methods This study used the Bruker MALDI Biotype system and the mass spectra models generated by 20 B. fragilis reference strains (10 cfiA-positive and 10 cfiA-negative) in the ClinProTools software to identify 404 B. fragilis (71 cfiA-positive and 333 cfiA-negative) clinical isolates. The ability of the CarbaNP assay to detect IS-mediated activation of the cfiA gene was assessed and the results obtained by molecular analysis were used as reference methods.
Results The support vector machine model generated by ClinProTools was found to be the most reliable algorithm for differentiation of cfiA-positive and cfiA-negative B. fragilis subgroups. Using the direct transfer method, all but one cfiA-negative isolates were correctly identified to the two subgroups by the model. The correct identification of the cfiA-negative isolate was obtained upon retesting by the extraction method. Of the 81 cfiA-positive isolates, PCR and sequencing showed that 30 had an IS element providing the promoter for activation of cfiA. With regard to the presence of the IS element, the CarbaNP test in the cfiA upstream region had 100% sensitivity, 80.4% specificity, 75.0% positive predictive value and 100% negative predictive value.
Conclusions The combination of MALDI-TOF MS and the CarbaNP assay can be applied in diagnostic clinical laboratory for rapid identification of B. fragilis with IS element-activated cfiA gene.
- ANTIMICROBIAL RESISTANCE
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Handling editor Tahir Pillay
Contributors All authors contributed to the study and are in agreement with the content of the manuscript. P-LH, CWST and K-HC designed and coordinated the study. P-LH and CWST provided the bacterial isolates. C-YY, L-YH, JHKC, ELYL, SWUL, K-HC performed the experiments. P-LH wrote the manuscript and other authors critically reviewed and corrected the manuscript.
Funding This work was supported by a grant from the Health and Medical Research Fund (HKM-15-M10) of the Food and Health Bureau of the Hong Kong Special Administrative Region.
Competing interests None declared.
Provenance and peer review Not commissioned; externally peer reviewed.