Ann Lab Med.  2020 May;40(3):209-215. 10.3343/alm.2020.40.3.209.

Evaluation of Xpert Carba-R Assay v.2 to Detect Carbapenemase Genes in Two Hospitals in Korea

Affiliations
  • 1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea. deyong@yuhs.ac
  • 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.

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.

Keyword

Xpert Carba-R v.2; Performance; Carbapenemase-producing Enterobacteriaceae; KPC; NDM; Infection control
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