Ann Lab Med 2020; 40(3): 209-215  https://doi.org/10.3343/alm.2020.40.3.209
Evaluation of Xpert Carba-R Assay v.2 to Detect Carbapenemase Genes in Two Hospitals in Korea
Jung-Hyun Byun, M.D.1,2, Young Ah Kim, M.D.3, Milee Kim, M.T.1, Bomi Kim, M.T.1, Jun Yong Choi, M.D.4, Yoon Soo Park, M.D.5, and Dongeun Yong, M.D.1
1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea; 2Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea; 3Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea; 4Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea; 5Department of Internal Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
Corresponding author: Dongeun Yong, M.D.
Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
Tel.: +82-2-2228-2442 Fax: +82-2-364-1583 E-mail: deyong@yuhs.ac
Received: February 16, 2019; Revised: August 4, 2019; Accepted: November 22, 2019; Published online: May 1, 2020.
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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.
Keywords: Xpert Carba-R v.2, Performance, Carbapenemase-producing Enterobacteriaceae, KPC, NDM, Infection control



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