Distribution of Carbapenemase Genes among Clinical Isolates of Escherichia coli and Klebsiella spp. in a Tertiary Care Centre: A Cross-sectional Study

Abstract

Introduction: Carbapenemase-Producing Enterobacterales (CPE), especially Escherichia coli and Klebsiella spp., have become a serious global health concern due to their role in nosocomial infections, limited treatment options, and high mortality. Resistance is primarily mediated by carbapenemase genes, often undetected by conventional phenotypic methods. Early molecular tool detection is crucial for effective infection control and antimicrobial stewardship. Aim: To detect carbapenemase-producing E. coli and Klebsiella spp. using both phenotypic mCIM (modified carbapenem inactivation method) and eCIM (EDTA-modified carbapenem inactivation method) and genotypic Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) methods at a tertiary healthcare centre in Central India. Materials and Methods: This cross-sectional study was conducted in the Department of Microbiology, Jawaharlal Nehru Medical College, Sawangi, Wardha, Maharashtra, India. A total of 205 non-duplicate clinical isolates were collected from June 2022 to June 2024. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disk diffusion method as per Clinical and Laboratory Standards Institute (CLSI) 2022 guidelines. Carbapenemase production was confirmed phenotypically using mCIM and eCIM. Genotypic detection of carbapenemase genes (blaNDM, blaOXA-48, blaKPC, blaVIM, and blaIMP) was done by real-time PCR. Data were analysed using descriptive statistics; p-value<0.05 was considered significant. Results: Out of 205 isolates, 115 (56.1%) were confirmed as carbapenemase producers, with 94 (81.7%) identified as Metallo-β-Lactamase (MBL) producers and 21 (18.3%) as serine carbapenemase producers. RT-PCR detected carbapenemase genes in 60 of 73 phenotypically positive isolates (82.19%). blaNDM gene was most prevalent 41 (56.16%), followed by blaOXA48 35 (47.94%), blaKPC 11 (15.06%), blaVIM 9 (12.32%), and blaIMP 1 (1.36%). Co-occurrence of these genes was also common, with 13 isolates showing both NDM and OXA-48. Conclusion: The study highlights a high prevalence of NDM and OXA-48 carbapenemase genes among E. coli and Klebsiella spp. in Central India. The predominance of MBLs emphasises the urgent need for routine molecular diagnostics, stringent infection control, and antibiotic stewardship to curb the spread of these highly resistant organisms. The combination of phenotypic and rapid genotypic methods enables timely identification of resistance patterns, which is essential for targeted therapy, infection control, and healthcare settings.