Evaluation of three commercial assays for rapid detection of genes encoding clinically relevant carbapenemases in cultured bacteria

Abstract

Abstract Objectives To assess the performance of three commercial molecular assays for detecting major families of carbapenemases in pure bacterial isolates. Methods A panel of 450 isolates with previously defined carbapenem resistance mechanisms was tested using the Check-Direct CPE kit, the eazyplex® SuperBug complete A kit and the Xpert® Carba-R kit. Isolates included 438 Enterobacteriaceae and 12 Pseudomonas spp. comprising 100 isolates each with KPC, NDM, VIM or OXA-48-like enzymes, two isolates producing both an NDM and an OXA-48-like enzyme, 24 IMP producers and 24 isolates without a known carbapenemase gene. Discordant results (commercial versus in-house) were investigated using in-house PCR and amplicons were sequenced to define the carbapenemase allele present. Results All three commercial assays detected all isolates with KPC, VIM, NDM and classic OXA-48 carbapenemases (no false-negatives). Isolates producing the OXA-181 variant (n = 18) were not detected by the Xpert® Carba-R kit or the eazyplex® SuperBug complete A kit, but were subsequently detected with modified versions of these kits. Only the Xpert® Carba-R kit could detect IMP carbapenemases, although this was limited to the IMP-1 subgroup. Invalid or false-positive results were either not observed when following the manufacturer's protocols or were eliminated by making simple interpretative adjustments to allow use with bacterial isolates rather than clinical samples. Conclusions Commercial assays offer a reliable means of detecting bacteria with clinically significant carbapenemases. Coverage of some assays required expansion to maximize the sensitivity for OXA-48-like carbapenemases. Choice will ultimately depend on preferred gene coverage, intended throughput, cost and ability to fit into local workflows.