Genomic and phenotypic evaluation of antibiotic resistance Escherichia coli from wastewater samples in a Western Indian megacity indicate higher multiple antibiotic resistance index and clinical relevant sequence types

Antimicrobial resistance (AMR) is a serious global threat, with antibiotic-resistant bacteria (ARB) posing major public health risks. Escherichia coli, a common uropathogen, has become increasingly resistant to multiple antibiotics, complicating treatment in both healthcare and community settings. Carbapenem-resistant E. coli is particularly challenging due to its multiple resistance mechanisms. Wastewater analysis offers insights into ARB prevalence in communities, as wastewater serves as both a reservoir and conduit for these bacteria, impacting human and environmental health. Furthermore, studying the wastewater of an urban environment like Pune, India, provides a unique backdrop for studying antibiotic-resistant bacteria, as the high population density and diverse healthcare facilities contribute to a dynamic exchange of microbial flora.This study aimed to isolate and characterize ARB from 88 wastewater samples across 11 sewage treatment plants in Pune, India, from October 2023 to May 2024. E. coli isolates were identified and tested for antimicrobial susceptibility, with a subset analyzed using real-time PCR and whole genome sequencing. Findings revealed a predominance of carbapenem-resistant E. coli, notably harboring blaNDM-5, blaOXA-48, and other beta-lactamase genes. The most common sequence type was ST361, associated with multiple resistance genes and virulence factors. A strong positive association with virulence factors and pathogenecity is present. Furthermore, the resistance of isolates was compared with previous studies, which include clinically isolated E. coli, to demonstrate the correlation with clinical AMR. This study highlights the presence of clinically relevant E. coli isolates in community wastewater. The results indicate that wastewater surveillance can serve as an efficient tool for monitoring antibiotic-resistant profiles of bacterial pathogens for public health. This study underscores wastewater surveillance as a valuable tool for tracking antibiotic-resistant pathogens, supporting public health efforts in AMR management.