Rapid Identification of Carbapenemase Genes Directly from Blood Culture Samples

Background/Objectives: The rapid identification of carbapenemase genes directly from positive blood culture (BC) samples shortens the time needed to initiate optimal antimicrobial therapy for Carbapenemase-Producing Enterobacterales (CPE) infections. Several commercial automated PCR systems are available for detecting CPE resistance genes but are expensive. The Xpert^® Carba-R assay (Cepheid GeneXpert System) has high sensitivity and specificity for the detection of carbapenamase genes from bacterial colonies or rectal swabs, with an affordable price. This assay was not used for positive BC testing of CPE resistance genes. Whole-Genome Sequencing (WGS) for resistance genes can be used as the gold standard at a research level. In this study, we evaluated the performance of the Xpert^® Carba-R assay for the early detection of carbapenamase genes directly from positive BCs, using WGS as the gold standard. Methods: A prospective observational study was conducted at Children's Cancer Hospital-Egypt (CCHE-57357). All positive BCs underwent direct gram staining and conventional cultures. A total of 590 positive BCs containing Gram-negative rods (GNRs) were identified. The Xpert^® Carba-R assay was used to detect carbapenemase genes directly from the positive BC bottle compared with WGS results. Results: Among the 590 GNR specimens, 178 were found to carry carbapenemase genes using the Xpert^® Carba-R assay, with results obtained in approximately one hour. The main genotypes detected were bla_NDM, bla_OXA-48-like, and dual bla_NDM/bla_OXA-48-like at 27%, 29%, and 33%, respectively. The agreement between Xpert^® Carba-R assay and WGS results was almost perfect for the genotype resistance pattern of isolates and individual gene detection. Conclusions: The use of the Xpert^® Carba-R assay directly from BC bottles was an easy-to-use, time-saving, affordable tool with high accuracy in identifying carbapenemase genes and, thus, shortens the time needed to initiate optimal antimicrobial therapy for CPE infections.