# 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

## TL;DR

This study analyzes E. coli isolates from a hospital in India to understand their resistance to antibiotics and virulence traits, revealing high levels of drug resistance and concerning bacterial clones.

## Contribution

The study provides genomic insights into E. coli clinical isolates in India, highlighting high-risk lineages with combined virulence and multidrug resistance.

## Key findings

- 90% of isolates showed multidrug resistance, with universal resistance to fluoroquinolones and third-generation cephalosporins.
- 76% of isolates carried carbapenemase genes, and the most common sequence type was ST167.
- Virulence factors like fim, pap, and iutA were prevalent, with no diarrheagenic E. coli pathotypes identified.

## Abstract

Introduction

Escherichia coli (E. coli) 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 E. coli lineages from India remain limited. This study aimed to characterize the population structure, AMR determinants, virulence profiles, and plasmid content of clinical E. coli isolates using whole-genome sequencing (WGS).

Methods

An exploratory study was conducted on 50 clinical E. coli 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 (blaNDM-1, blaNDM-5, blaOXA-181) 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 (fim, pap, afa) and iron acquisition systems (iutA, fyuA, iroN). No classical diarrheagenic E. coli pathotypes were identified. IncF-type plasmids were the most prevalent.

Conclusion

This study highlights the alarming convergence of virulence and multidrug resistance among dominant E. coli 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.