Xpert Carba-R Detects Carbapenemase Genes Directly from Sputum in Under 2 Hours
A multicenter study evaluated the Cepheid Xpert Carba-R multiplex PCR for detecting five major carbapenemase genes (KPC, NDM, VIM, OXA-48, IMP) directly from sputum specimens. The assay reduced turnaround time from 56-84 hours to under 2 hours compared to culture plus PCR, with concordance rates of 88% for dominant resistance genes. Rapid carbapenemase identification from respiratory specimens could accelerate targeted therapy and infection control for CRE.
The original study
Multicenter Evaluation of the Xpert Carba-R Assay for Detection and Identification of Carbapenemase Genes in Sputum Specimens.
- Authors
- Cai Z, Tao J, Jia T, Fu H, Zhang X, Zhao M, et al.
- Journal
- Journal of clinical microbiology
- Type
- Journal Article, Multicenter Study, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't
- PMID
- 32522829
Original abstract
Rapid diagnosis of infections caused by carbapenem-resistant Enterobacteriaceae (CRE) is crucial for proper treatment and infection control. The Xpert Carba-R assay is a qualitative multiplex real-time PCR method that qualitatively detects and differentiates five common carbapenemase genes (blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP) directly from rectal swabs or purified colonies within approximately 1 h. We performed a multicenter evaluation of the investigational use of the Carba-R assay for detection and differentiation of carbapenemase genes from sputum specimens in patients with a clinical diagnosis of pneumonia. The intra- and interassay coefficients of variation values for the Carba-R assay were 0.2% to 2.0% and 1.4% to 2.3%, respectively. A total of 301 sputum specimens were collected and tested. Compared to bacterial culture followed by PCR identification of resistance genes from colonies, the Carba-R assay reduced turnaround time from 56 to 84 h to less than 2 h. Carbapenemase genes were detected by the Carba-R assay in Klebsiella pneumoniae (n = 236), Escherichia coli (n = 22), Enterobacter cloacae (n = 23), Klebsiella oxytoca (n = 8), Serratia marcescens (n = 6), Citrobacter freundii (n = 4), and Klebsiella aerogenes (n = 2). The Carba-R assay detected 112 blaKPC (33.5%), 70 blaNDM (21.0%), 8 blaIMP (2.4%), and 2 blaVIM (0.6%) genes, with positive percent agreement, negative percent agreement, and concordance rates of 92.9%, 86.7%, and 88.3%, respectively, for the dominant blaKPC and 85.0%, 87.8%, and 87.4%, respectively, for the blaNDM genes. Neither method detected the blaOXA-48 carbapenemase gene. The convenient, rapid, and simple characteristics of the Xpert Carba-R assay make it a potential tool for CRE detection and identification directly in sputum specimens.