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

Climate change and health are closely linked to urban wastewater used for irrigation. Sewage treatment plants (STPs) provide ideal environments and niche availability for the transmission of antibiotic resistance genes (ARGs) among pathogenic and non-pathogenic bacteria. In this study, we examined the differential effect of sewage processing methods from the inlet to the outlet on the microbial diversity and antibiotic resistomes of 26 STPs in the urban sewage network of Bengaluru, India. We screened 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 with outlets. 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 correlations between ARGs and bacteria compared with outlet samples. Our findings serve as a baseline study that could aid in the quantification of genes from both culturable and non-culturable taxa and will assist in the development of policies and strategies to address water quality issues associated with the use of recycled water.