Resistome profile of a multidrug-resistant Escherichia coli isolated from an urban river body under high anthropogenic stress

Emergence of antimicrobial resistance (AMR) in freshwater ecosystems like rivers is a growing public health crisis driven by the release of untreated household, hospital and agricultural sewage. These contaminated freshwater sources have become reservoirs for resistant bacteria, facilitating the spread of these pathogens across different environmental zones. The continuous and unchecked influx of drugs, heavy metals and disinfectants from sewage has exerted selective enrichment of resistomes in aquatic pathogens. These resistance genes are shared and spread through plasmids or bacteriophage-derived elements and several metagenomic studies have reported the isolation of bacteria harbouring these resistance determinants in polluted rivers. The implications of such findings on public health are severe, especially on communities which are reliant on river waters for drinking and recreational activities. We were able to isolate and characterize a MDR Escherichia coli strain through whole genome sequencing. Presence of over 50 chromosomal resistance genes with diverse AMR gene families [e.g. major facilitator superfamily (MFS), resistance-nodulation-division (RND) family] and resistance mechanisms along with phage elements from the order Caudovirales , highlighted AMR risks in river reaches within dense human and livestock population. APH(3’) and quinolone resistance protein family genes were found in associated plasmids implying their transfer potential within related bacterial communities. Collectively, the findings of this study constitutes a first-hand report on the presence of a high-risk, broad spectrum resistant pathogen, stressing over the importance of expanding the environmental resistome tracking.