Detection of plasmid-mediated mcr-1 gene in multidrug-resistant Escherichia coli from clinical specimens at a tertiary hospital in Nepal

Abstract Background: The emergence of antibiotic resistance, particularly plasmid-mediated colistin resistance, poses a critical threat to global public health, given colistin’s role as a last-resort antibiotic for treating multidrug-resistant (MDR) bacterial infections. Despite its significance, data on colistin resistance and the prevalence of mobile colistin resistance ( mcr ) genes in Nepal are scarce. This study aims to investigate the occurrence of plasmid-mediated mobilized colistin resistance genes mcr-1 and mcr-2 in MDR Escherichia coli isolates from clinical specimens, highlighting the burden of resistance and its clinical implications in Nepalese context. Methods: A hospital-based cross-sectional study was conducted at Sukraraj Tropical Infectious Disease Hospital in Kathmandu from March to August 2022. A total of 1358 clinical specimens were processed using standard microbiological techniques. Antibiotic susceptibility testing followed the Kirby-Bauer disk diffusion method per the 2016 Clinical and Laboratory Standards Institute guidelines. The minimum inhibitory concentration (MIC) for colistin was determined via agar dilution method. Colistin-resistant strains were further investigated for the detection of mcr-1 and mcr-2 genes using endpoint polymerase chain reaction. Results: A total of 86 E. coli isolates were recovered with a prevalence rate of 6.3% (86/1358). Higher growth rates of E. coli were observed among females (9.0%, 56/620), individuals aged 46–60 years (8.5%, 23/271), and in pus samples (3 out of 7). Majorities of the isolates exhibited high resistance rates towards beta-lactam antibiotics and cotrimoxazole, with 81.4% (70/86) classified as MDR. The MIC of colistin was ≥ 4 μg/mL in 7 isolates. The prevalence of extended-spectrum beta-lactamase (ESBL)-, metallo-beta-lactamase (MBL)-, and klebsiella pneumoniae carbapenemases-producing isolates was 40.7% (35/86), 14.0% (12/86), and 1.2% (1/86), respectively. The mcr-1 gene was detected in 5 colistin-resistant isolates, while mcr-2 was not identified. Notably, all ESBL- and MBL-producing isolates were also MDR, with higher proportions of ESBL-producing (4 out of 5) and MBL-producing (1 out of 5) strains among those harboring the mcr-1 gene. Conclusions: This study highlights a concerning prevalence of mcr-1 -mediated colistin resistance in E. coli isolates, compounded by co-resistance to other critical antibiotics such as beta-lactams and carbapenems. The findings underscore the urgent need for enhanced surveillance, antimicrobial stewardship, and research into colistin resistance mechanisms for preventing further escalation of the resistance burden.