Highly resolved community sewage metagenomics unveiling landscape and transmission patterns of antibiotic resistome in Hong Kong populations

The increasing global burden of antimicrobial resistance (AMR) has been identified as a critical public health crisis, necessitating the development of robust, real-time surveillance frameworks to evaluate AMR dynamics. Sewage surveillance is emerging as a promising tool that utilizes sewage fingerprinting to provide comprehensive and unbiased information on antibiotic resistance genes (ARGs) within human populations. Here, we conducted a large-scale, year-long field surveillance of resistome in the community sewage using both short- and long-read metagenomic sequencing. We examined samples collected from 95 geographically distributed sites across Hong Kong, covering a population of 4.8 million residents, during summer and winter seasons. Our findings revealed distinct seasonal patterns through high-resolution resistome profiling. We found that the resistome structures shifted from the community sewage collected at sewer manholes to the influent of wastewater treatment plants (WWTPs), driven by taxonomic variation. Notably, community sewage exhibited a significantly higher similarity to the resistome of human feces than WWTP influent, which provides insights for selecting suitable sampling sites for epidemiological ARG surveillance. The application of long-read sequencing markedly enhanced our understanding of the phylogenetic diversity of ARG hosts and uncovered a broad spectrum of potentially mobile ARGs with varied genetic backgrounds. Furthermore, we observed multiple local ARG transmission patterns and subsequently evaluated their potential threats to public health based on the gene trees to inform future epidemiological control strategies. Overall, this work expands our current understanding of community sewage for population-level AMR monitoring and establishes a baseline for advancing sewage surveillance efforts to better combat AMR. Copyright © 2026 The Author(s).