Diversity of antibiotic resistance genes increases in urbanized lakes: A multi-tool screening

Antimicrobial resistance (AMR) threatens to cause up to 10 million deaths annually by 2050 if no action is taken. Using shotgun sequencing, we examined the eco-evolutionary dynamics of AMR across urban-rural environment gradients in lake water and sediments, a farm pond and a wastewater treatment plant (WWTP). ARGs were identified using multiple databases and five bioinformatic tools, detecting up to 18 ARG classes-more than any single tool alone. ARG diversity was higher in urban lake sediments, urban waters, and wastewater compared to rural lake sediments and water. Among all environments, urban lake water showed the highest overall ARG abundance, second only to wastewater, and this pattern held across all ARG classes, except for aminoglycoside resistance, which was most prevalent in rural lake sediments. These findings highlight multi-tool ARG screening efficiency, WWTPs and urban sediments as major ARG reservoirs, and emphasize the need for enhanced urban-rural AMR surveillance.