Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India

Area of Science:

• Environmental microbiology
• Molecular biology
• Public health

Background:

• Antimicrobial resistance (AMR) is a global health threat, driven by the spread of antimicrobial resistance genes (ARGs).
• Sublethal antibiotic concentrations in dense microbial environments, like sewage, can promote ARG acquisition and transmission.

Purpose of the Study:

• To investigate sewage as a reservoir for ARGs and multidrug-resistant (MDR) bacterial pathogens.
• To assess the correlation between antibiotic concentrations, microbial diversity, and ARG richness in Indian sewage samples.
• To develop a rapid detection method for ARGs in sewage for surveillance purposes.

Main Methods:

• Analysis of 381 sewage samples from six Indian states for antibiotic concentrations, microbial diversity (ASVs), and ARG richness.
• Metagenomic and isolated genome sequencing (n=220 + 305) to identify ARGs and associated mobile genetic elements (MGEs).
• Comparative core genome analysis of MDR bacterial isolates (n=7166) to compare sewage-derived strains with clinical pathogens.

Main Results:

• Detected antibiotics from seven drug classes and over 2000 bacterial ASVs.
• Identified 82 ARGs linked to 80 MGEs, predominantly in MDR pathogens.
• Found significant genetic similarity between sewage-derived MDR strains and clinical pathogens, confirming sewage as an ARG reservoir.

Conclusions:

• Sewage is a critical reservoir for ARGs and facilitates the evolution and spread of AMR pathogens.
• Genetic exchange in sewage contributes to AMR in both community and healthcare settings.
• A developed dipstick-based assay offers a viable tool for sewage surveillance in low-resource regions.