Prevalence of Class 1 integron in disease-causing carbapenem-resistant Escherichia coli in a tertiary hospital in Kathmandu, Nepal

Background High prevalence of carbapenem resistance genes have been abundantly reported within clinical E. coli in Nepal but their co-prevalence with class-1 integron is poorly documented. These Class I Integrons play pivotal role in evolution and spread of antimicrobial resistance (AMR). Therefore, it is necessary to highlight their epidemiological significance, so this study determined the prevalence of Class 1 integrons within Carbapenem resistance Escherichia coli (CREc) population. Methods Fifty two clinical E. coli with confirmed resistance to Meropenem were collected between January 2020 to April 2022 in Kathmandu Model Hospital, and undergone antimicrobial susceptibility testing for 11 antimicrobial classes. Carbapenemase production was confirmed by eCIM and mCIM methods. Presence of Class I integron and carbapenemase genes, blaNDM-1, blaKPC, blaIMP, blaVIM, blaOXA-23, blaOXA-48, was confirmed by PCR method. Results The result revealed 92.3% (n=48/52) of the isolates harbored intI1 gene. Among integron-positive population, 97.9% (n=47/48) were carbapenemase producers which were further identified as metallo β-lactamase (MBL) producers (82.9%, n=39/47) and serine β-lactamase (SBL) producer (17%, n=8/47). Carbapenemase gene blaNDM-1 (79.2%, n=38/48) was highly prevalent within integron-positive isolates, followed by blaOXA-23 (62.5%, n=30/48) and blaOXA-48 (54.2%, n=26/48). All integron-positive CREc isolates were resistant to minimum 16 antibiotics tested, but were susceptible to Colistin, Polymixin B, and Tigecycline. Conclusion In conclusion, Class 1 integrons were highly prevalent within clinical CREc in Nepal, and their co-prevalence with other CRE gene is concerning due to possibility of wider spread. Therefore, an in depth genomic analysis of Class 1 integrons is needed to understand the integron mediated AMR in high risk clones like CREc and inform intervention measures to stop spread of such pathogens. ### Competing Interest Statement The authors have declared no competing interest.