Background: As the spread of carbapenemase-producing Enterobacteriaceae poses a critical threat to public health, rapid detection of carbapenemase genes is urgently required for prompt initiation of appropriate antimicrobial therapy and infection control. We evaluated the performance of Xpert Carba-R v.2 (Cepheid, USA) compared with that of culture-based conventional PCR. Methods: Using the results of 5,479 consecutive clinical rectal swabs, discrepant analysis (enriched culture followed by PCR) was performed for all discordant samples (N = 100), which were Carba-R v.2-positive and culture-negative. Results: Among the samples, 206 carbapenemase genes (3.6%) were detected by Carba-R v.2. The sensitivity and specificity were 95.0% and 98.1%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) were 49.0% and 99.9%, respectively. Following discrepant analysis, the PPV increased to 73.5% and the low PPV (8.1%) of the 86 non-KPC improved to 48.8%. Among the 105 discrepancies, NDM was the most frequently observed (N = 56), followed by KPC (N = 26), VIM (N = 10), IMP (N = 8), OXA-48 (N = 5). The threshold cycle values between discordant vs. concordant and resolved groups were significantly different (P < 0.001). Conclusions: Carba-R v.2 is a rapid and sensitive method for detecting carbapenemase-encoding genes compared with culture-based conventional PCR. Most of our discrepant results were non-KPC genes. Thus, the clinical significance of the non-KPC positive cases detected by Carba-R v.2 should be investigated. This assay would be useful for deciding whether to isolate pre-exposed patients in hospital settings, based on the high specificity and NPV.
Bibliographical noteFunding Information:
This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries through the Agricultural Microbiome R&D Program, funded by the Ministry of Agriculture, Food and Rural Affairs (918003-4); by the Korea Health Technology R&D Project through the KHIDI funded by the Ministry of Health & Welfare, Korea (grant number HI17C180,7); and by the BioNano Health Guard Research Center funded by the MSIP of Korea as a Global Frontier Project (H-GUARD_2014M3A6B2060509). This study was also partly supported by Cepheid. The funders had no role in study design, data collection, and interpretation, or in the decision to submit the work for publication.
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