Chlorination-driven selection of resistant pathogens and mobile genetic elements exacerbates antibiotic resistance risks in drinking water treatment

The dissemination of Antibiotic resistance genes (ARGs) in drinking water systems poses public health risks; treatment impacts on pathogen dynamics remain unclear. In this study, two treatment trains-PK (sand filtration, ozonation-activated carbon, 5 % NaClO)and CX(ozonation-activated carbon, ultrafiltration, and 10 % NaClO) were compared through metagenomics analysis. Chlorination reduced microbial α-diversity but selected for divergent pathogens: CX-Treated Water (TW) was enriched with Salmonella enterica, Escherichia coli, and Erwinia amylovora, while PK retained Xanthomonas oryzae and Mycobacterium tuberculosis. Virulence gene tufA persisted, with 43 human-associated virulence factors being differentially expressed after disinfection. ARG analysis revealed high abundances of bacitracin and multidrug resistance gene (MRG) in early treatment stages for both lines. Chlorination paradoxically enriched these ARGs in TW, particularly MRG, which increased by 5.99 and 126.12 times in PK and CX, respectively. Mobile genetic elements (MGEs), particularly IS91, rebounded after disinfection and strongly correlated with the dissemination of ARGs (R > 0.9, p < 0.05). Higher concentrations of hypochlorite doses in CX-DWTP amplified plasmid associated Rep7/IS91 abundances, increasing ARG transmission risks. These findings revealed that aggressive disinfection selected resistant pathogens, enriches virulence determinants, and facilitated the dissemination of ARGs via MGEs, highlighting the need for optimized disinfection strategies to safeguard water biosafety.