Wastewater Genomics Reveals Seasonal Antibiotic Resistance Trends

A year-long metagenomic surveillance study in Pune by CSIR-The National Chemical Laboratory (NCL), Fluid Analytics and Partners, demonstrates how wastewater can serve as a powerful population-scale early-warning system for antimicrobial resistance (AMR). Researchers analyzed 190 monthly wastewater influent samples collected between December 2022 and December 2023 using nanopore shotgun sequencing, generating nearly 88 Gbp of genomic data.

The analysis identified a highly diverse microbial ecosystem spanning 157 bacterial phyla and more than 3,200 genera, with Proteobacteria dominating the community. Clear seasonal shifts were observed, including elevated Streptococcus abundance coinciding with SARS-CoV-2 infection surges in early 2023.

Critically, the study detected 637 distinct antimicrobial resistance genes across 29 antibiotic classes. Resistance associated with multidrug therapies, beta-lactams, macrolides, and tetracyclines was most prevalent, particularly among WHO-priority pathogens such as Enterobacteriaceae and Pseudomonas. Normalized temporal analysis revealed pronounced seasonal variation in resistance gene abundance, peaking during winter months—likely reflecting increased antibiotic usage for respiratory illnesses.

By integrating viral load data with resistance profiles, the study highlights complex interactions between infectious disease outbreaks and AMR dissemination. The findings reinforce wastewater-based genomics as a scalable, non-intrusive surveillance approach to track emerging resistance trends and inform proactive public-health strategies in rapidly growing urban centers across India.