Comparative epidemiology, virulence profiling, and antimicrobial resistance of diarrheagenic Escherichia coli in pediatric diarrhea across secondary and tertiary healthcare settings in North

Abstract Purpose This study aimed to investigate the distribution of diarrheagenic Escherichia coli (DEC) pathotypes, virulence profiles, hybrid strains, and antimicrobial resistance (AMR) in children across secondary (CRHSP Ballabgarh) and tertiary (AIIMS, New Delhi) healthcare settings in North India. Methods Fecal specimens from 270 children (≤ 12 years) with acute diarrhea were prospectively collected between September 2024 and June 2025. Following Escherichia coli (E. coli) identification via MALDI-TOF MS, PCR targeted eleven virulence genes to assign pathotypes. Antimicrobial susceptibility was determined using the VITEK-2 Compact system following CLSI 2023 guidelines. Results Out of 200 E. coli isolates in our study, 93 (46.5%) were confirmed as DEC, comprising 73 classical pathotypes and 20 hybrid strains (10%). DAEC and EAEC were the most prevalent pathotypes, followed by ETEC, EPEC and EIEC. Hybrid strains, most frequently ETEC/DAEC, were predominantly found in the secondary healthcare settings. High resistance rates were observed for β-lactam antibiotics, including ceftriaxone (63.3%–100%), whereas carbapenems, colistin, and tigecycline remained highly effective. Clinically, ETEC was associated with watery diarrhea and EIEC with bloody stools. Conclusion DEC, specifically DAEC and EAEC, is a major contributor to pediatric diarrhea in North India. The presence of diverse hybrid pathotypes and high AMR levels highlights the critical need for integrated molecular surveillance and robust antimicrobial stewardship across varying healthcare levels.