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

• Byun JH
• Kim YA
• Kim M
• Kim B
• Choi JY
• Park YS
• Yong D

• KMID: 2466013
• DOI: http://doi.org/10.3343/alm.2020.40.3.209

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

MeSH Terms

Enterobacteriaceae
Humans
Infection Control
Korea*
Methods
Polymerase Chain Reaction
Public Health
Sensitivity and Specificity

Figure

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  Fig. 1 Study flow chart and discrepant analysis protocol.Abbreviation: TSB, tryptic soy broth.

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  Fig. 2 Comparison of number, median Ct value and interquartile range in (A) the concordant group at initial assay (25.4, 22.2–30.9), resolved discrepancy group after discrepant analysis (28.5, 22.3–31.7), and discordant groups (52, 35.0, 31.4–37.7) and (B) the concordant (24.4, 22.2–30.1) and discordant (35.5, 29.9–36.0) KPC groups and concordant (32.2, 27.5–34.6) and discordant (34.8, 31.3–36.5) NDM groups.Abbreviations: Ct, threshold cycle; KPC, Klebsiella pneumoniae carbapenemase; NDM, New Delhi metallo-β-lactamase.

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