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

BackgroundHigh 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. MethodsFifty-two clinical E. coli with confirmed resistance to Meropenem were collected between January 2020-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. ResultsThe 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 {beta}-lactamase (MBL) producers (82.9%, n=39/47) and serine {beta}-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. ConclusionIn 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.