Molecular Epidemiology of Escherichia coli Clinical Isolates From a Tertiary Care Hospital in Uttarakhand, India: Insights Into Antimicrobial Resistance (AMR) Burden, Virulence Profiles, and High-Risk Lineages

Introduction <i>Escherichia coli</i> (<i>E. coli</i>) is a major cause of extraintestinal infections and a leading contributor to antimicrobial resistance (AMR), particularly in low- and middle-income countries. The increasing convergence of multidrug resistance and virulence within high-risk clones poses serious challenges to treatment and infection control. Genomic data on circulating clinical <i>E. coli</i> lineages from India remain limited. This study aimed to characterize the population structure, AMR determinants, virulence profiles, and plasmid content of clinical <i>E. coli</i> isolates using whole-genome sequencing (WGS). Methods An exploratory study was conducted on 50 clinical <i>E. coli</i> isolates collected between January 2018 and October 2020 from diverse clinical specimens at a tertiary care teaching hospital in Uttarakhand, India. Antimicrobial susceptibility testing was performed using the VITEK 2 Compact system and interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. WGS was carried out on the Illumina MiSeq platform. In silico analyses included phylogrouping, multilocus sequence typing (MLST), serotyping, AMR gene detection, virulence factor profiling, and plasmid replicon typing. Results Multidrug resistance was observed in the majority (45/50 (90%)) of the isolates. Universal phenotypic resistance was noted to fluoroquinolones (50/50 (100%)) and third-generation cephalosporins (50/50 (100%)), while carbapenem resistance was detected in 35/50 (70%). Tigecycline and colistin retained in vitro activity in 47/50 (94%) and 50/50 (100%) isolates, respectively. Genomic analysis identified extended-spectrum beta-lactamases (ESBL) genes in all isolates and carbapenemase genes (<i>bla_NDM-1</i> , <i>bla_NDM-5</i> , <i>bla_OXA-181</i> ) in 38/50 (76%), with high genotype-phenotype concordance. The predominant sequence type was ST167 (15/50 (30%)), followed by ST410, ST648, ST405, and ST131. Virulence profiling demonstrated predominance of ExPEC-associated adhesins (<i>fim</i>, <i>pap</i>, <i>afa</i>) and iron acquisition systems (<i>iutA</i>, <i>fyuA</i>, <i>iroN</i>). No classical diarrheagenic <i>E. coli</i> pathotypes were identified. IncF-type plasmids were the most prevalent. Conclusion This study highlights the alarming convergence of virulence and multidrug resistance among dominant <i>E. coli</i> clones in a tertiary care setting in India. The findings underscore the value of WGS-based surveillance in guiding antimicrobial stewardship and strengthening infection control strategies.