More than half of the microbial genomes recovered from urban wastewater are potentially new, revealing a largely unexplored reservoir of environmental bacteria. Credit: Subhra Priyadarshini
Wastewater flowing through India’s largest cities carries a vast and dynamic reservoir of antimicrobial resistance (AMR), much of it embedded in previously uncharacterised microbes, a large metagenomic study shows1.
Researchers from the CSIR–Centre for Cellular and Molecular Biology, the CSIR–National Environmental Engineering Research Institute and collaborating institutes analysed 447 wastewater samples collected over two years (2022–2024) from 19 sites across four metropolitan cities. Using shotgun metagenomics, they mapped microbial communities, resistance genes and mobile genetic elements at unprecedented scale.
Microbial compositions differed markedly between cities, reflecting local environmental and human influences. However, patterns of resistance genes were more uniform, suggesting widespread dissemination across urban centres. A striking 53–70% of reconstructed microbial genomes were potentially novel, pointing to a large, unexplored reservoir of environmental bacteria.
The study identified abundant resistance genes against commonly used antibiotics such as tetracyclines and beta-lactams. Many of these genes were closely associated with mobile genetic elements — DNA segments that can move between organisms — raising concern about their potential to spread rapidly across bacterial species.
Network analyses further revealed that specific microbial communities disproportionately contribute to resistance gene pools, with city-specific ecological structures shaping how these genes circulate.
The findings highlight wastewater as a critical interface where microbial diversity, human activity and antibiotic use converge, enabling the persistence and spread of resistance. Integrating such surveillance into public health systems could improve early detection and inform strategies to curb the global AMR threat.
