Metagenomic analysis reveals differential effects of sewage treatment on the microbiome and antibiotic resistome in Bengaluru, India

Abstract Background Climate change and health are closely linked to urban wastewater. In India, water security is a pressing issue. Water scarcity and decreased availability of agricultural water have led to a growing interest in using recycled irrigation water. Sewage treatment plants (STPs) provide environments that present great ecological opportunities, as well as niche availability for the transmission of antimicrobial resistance genes (ARGs) among pathogenic and non-pathogenic bacteria. Reusing treated wastewater for irrigation can provide both economic and environmental advantages, as wastewater is a valuable source of nutrients. However, there is limited monitoring of treated wastewater parameters and its impact on ecosystem health. Methods In this study, we conducted a metagenomic analysis of the microbial diversity and antibiotic resistomes of 26 STPs in the urban sewage network of Bengaluru, India. We examined the differential effect of sewage processing methods from the inlet to the outlet of STPs. Results The overall pattern of microbiome diversity showed no change with seasons, there were temporal differences and a significant reduction in ARGs. We screened of 478 ARGs and found 273 ARGs in wastewater, including clinically relevant genes such as CTX-M, qnr, sul-1, and NDM-1, which confer resistance to six major classes of antibiotics. The richness of ARGs was higher in sewage inlets compared to outlets, and there was significant variation in the clustering of ARGs among STPs, but not among sewage processing methods. We observed a downward shift in drug classes from inlet to outlet samples, except for aminoglycosides, beta-lactams, MLSB, and tetracycline. Inlet samples exhibited more complex and dense correlations between ARGs, and bacteria compared to outlet samples, indicating a higher diversity of ARGs in the sewage inflow. Conclusions Our findings serve as a baseline study that could aid in the quantification of genes from both culturable and nonculturable taxa. These findings will assist in the development of policies and strategies to address water quality issues such as the possible persistence of bacterial, viral, and protozoan pathogens associated with the use of recycled water. This is crucial for mitigating the impact of wastewater on the ecosystem health.