Open AccessMulticenter Evaluation of the Xpert Carba-R Assay for Detection and Identification of Carbapenemase Genes in Sputum Specimens
Author(s) -
Zhen Cai,
Tao Jia,
Tianye Jia,
Hongyu Fu,
Xin Zhang,
Mei Zhao,
Hong Du,
Hua Yu,
Bin Shu,
Bin Huang,
Liang Chen,
Yi Tang,
Wei Jia,
Fengli Qu
Publication year - 2020
Publication title -
journal of clinical microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.349
H-Index - 255
eISSN - 1070-633X
pISSN - 0095-1137
DOI - 10.1128/jcm.00644-20
Subject(s) - klebsiella pneumoniae , biology , sputum , microbiology and biotechnology , enterobacter aerogenes , enterobacter cloacae , citrobacter freundii , klebsiella oxytoca , enterobacteriaceae , carbapenem , serratia marcescens , gene , escherichia coli , medicine , antibiotics , tuberculosis , genetics , pathology
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 ( bla KPC , bla NDM , bla VIM , bla OXA-48 , and bla IMP ) 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 bla KPC (33.5%), 70 bla NDM (21.0%), 8 bla IMP (2.4%), and 2 bla VIM (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 bla KPC and 85.0%, 87.8%, and 87.4%, respectively, for the bla NDM genes. Neither method detected the bla OXA-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.