Evaluation of xpert carba-R assay v.2 to detect carbapenemase genes in two hospitals in Korea

Jung Hyun Byun, Young Ah Kim, Milee Kim, Bomi Kim, Jun Yong Choi, Yoon Soo Park, Dongeun Yong

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)209-215
Number of pages7
JournalAnnals of laboratory medicine
Volume40
Issue number3
DOIs
Publication statusPublished - 2020

Bibliographical note

Funding 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.

All Science Journal Classification (ASJC) codes

  • Clinical Biochemistry
  • Biochemistry, medical

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