Multicenter Evaluation of the Xpert Carba-R Assay for Detection and Identification of Carbapenemase Genes in Sputum Specimens

• Published in: Journal of clinical microbiology 2020-08, Vol.58 (9)
• Main Authors: Cai, Zhen, Tao, Jia, Jia, Tianye, Fu, Hongyu, Zhang, Xin, Zhao, Mei, Du, Hong, Yu, Hua, Shan, Bin, Huang, Bin, Chen, Liang, Tang, Yi-Wei, Jia, Wei, Qu, Fen
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - genetics; Bacteriology; beta-Lactamases - genetics; Carbapenem-Resistant Enterobacteriaceae; Enterobacteriaceae Infections - diagnosis; Humans; Sputum
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/JCM.00644-20

Rapid diagnosis of infections caused by carbapenem-resistant (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 ( , , , , and ) 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 (  = 236), (  = 22), (  = 23), (  = 8), (  = 6), (  = 4), and (  = 2). The Carba-R assay detected 112 (33.5%), 70 (21.0%), 8 (2.4%), and 2 (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 and 85.0%, 87.8%, and 87.4%, respectively, for the genes. Neither method detected the 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.