Antibiotic Contamination and AMR Dynamics in the Urban Sewage Microbiome: Insights from a Longitudinal surveillance

The emergence and spread of antibiotic resistance (AMR) in clinically important bacterial pathogens severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in a microbially dense environments. In this study, we used sewage samples (n=371) from six Indian cities between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. Our findings revealed the presence of antibiotics from seven drug classes and over 2000 bacterial ASVs. Metagenomic (n=220) and isolated genome sequences (n=305) of aerobic and anaerobic bacterial species identified 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs were predominantly found in multidrug-resistant bacterial pathogens. Comparative core genome analysis of multi drug-resistant (MDR) bacterial isolates (n=7166) showed a strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur, facilitating the evolution and spread of AMR pathogens within both community and healthcare settings. Additionally, the dipstick-based assay developed for detection of ARGs in the present study could be employed for sewage surveillance in low resource settings for better understanding of resistance prevalence.