Molecular diagnostic tools for detecting carbapenemase genes (NDM, KPC, OXA-48, VIM, IMP), extended spectrum beta-lactamase (ESBL) genes (e.g. CTX-M) and vancomycin resistance genes (vanA, vanB) are important for monitoring the spread of carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE), CTX-M-producing Enterobacteriaceae, and vancomycin-resistant enterococci (VRE). The purpose of this evaluation study is to compare the diagnostic performance of the Seegene AllplexTM Entero-DR Assay (Seegene assay) against in-use laboratory-developed tests (LDTs) for CP-CRE (detecting NDM, KPC and OXA-48-like using gel-based PCR) and VRE (vanA and vanB using real-time PCR). The Seegene assay detects NDM, KPC, OXA-48-like, VIM, IMP, CTX-M, vanA and vanB genes. Successful evaluation would enable a wider range of resistance gene detection.
Fifty bacterial strains from clinical specimens were studied; this included 31 carbapenem-resistant Enterobacteriaceae isolated between July 2023 and February 2024, and 19 enterococci isolated between 2013 and 2024. The isolates were selected based on phenotypic resistance to meropenem or vancomycin, respectively, by disk testing. Twenty-four isolates were positive for carbapenemase genes, 19 positive for vancomycin resistance genes, and 7 were negative by the LDTs. The CP-CRE and VRE LDTs were in agreement with the Seegene assay for all 43 LDT-positive isolates. The Seegene assay detected the ESBL gene CTX-M in 15 of the CP-CRE positive isolates. Among the seven LDT-negative isolates, the Seegene assay detected one isolate with an IMP gene, one with a CTX-M gene, and the remaining 5 isolates were negative for resistance genes.
In summary, the Seegene assay was in perfect agreement with the LDTs, except for genes that were contained in the Seegene assay but not the LDTs; it had an improved workflow and was more user-friendly. Further evaluation is necessary as this study did not include any direct testing of primary clinical specimens.