Multi-drug resistance patterns in water Escherichia coli: prevalence and co-occurrence associations

Abstract

Antimicrobial resistance (AMR) in the environmental water system is an emerging health issue of concern in the general population, especially in densely populated low and middle-income countries with poor wastewater management systems. This paper has explored the prevalence, diversity, and patterns of co-resistance of multidrug-resistant (MDR) Escherichia coli in three ecologically different urban water bodies in Dhaka, Bangladesh-Hatirjheel, Banasree, and the BRAC University water body during a longitudinal surveillance period of April to December 2025. A total of 150 environmental E. coli isolates were confirmed by biochemical IMViC characterization and colony PCR. The Kirby-Bauer disk diffusion technique was used to measure phenotypic susceptibility using eight clinical-relevant agents that represented the six antibiotic classes: fluoroquinolones, phosphonic acids, tetracyclines, beta-lactams, cephalosporins, and macrolides. Breakpoint interpretation was done in accordance with CLSI thresholds. Statistical analyses including- K-means clustering, Principal Component Analysis (PCA), Chi-square testing, Mann-Whitney U testing, and co-occurrence network analysis were conducted in R (version 4.3.1). The overall resistance burden was high: six out of eight antibiotics had resistance rates over 80% in all isolates. PCA indicated a strong spatial variation among sampling locations with the first two principal components having a cumulative (59%) total resistance variance. A statistically significant difference in the prevalence of resistance between broad-spectrum and narrow-spectrum antibiotics was seen at population level but not at isolate level (chi-square = 7.533, p =.006), which agrees with a generalized MDR phenotype. Co-occurrence network analysis revealed that there were two statistically significant pairwise co-resistance relationships; levofloxacin-azithromycin (0.473, p = 0.002), indicating possible cross-class resistance involving efflux pumps, and piperacillin-tazobactam-cefepime (0.452, p< 0.00). Inter-site comparison revealed that MDR was most prevalent in the BRAC University site followed by Banasree and finally, Hatirjheel. These results confirm the hypothesis that urban water bodies in Dhaka support high populations of MDR E. coli that is the result of multi-mechanistic resistance co-selection. The findings highlight the importance of the combination of environmental AMR surveillance, molecular characterization of resistance determinants, and evidence-based wastewater management policy in a One Health framework.