Wastewater study exposes scale of Antimicrobial Resistance in major Indian cities

Antimicrobial drugs like antibiotics kill bacteria and protect humans from many deadly infections. However, bacteria are increasingly becoming resistant to these drugs, also known as Antimicrobial Resistance (AMR), which is responsible for millions of deaths worldwide every year.

While it was long suspected that AMR is widespread in India, data on its local prevalence had been limited. Now, scientists at the CSIR–Centre for Cellular and Molecular Biology (CCMB), along with partner institutions, have shown that AMR is prevalent across all major Indian cities.

In the first comprehensive mapping of AMR using urban wastewater, the researchers analysed samples from 19 sites using a ‘shotgun metagenomics’ approach, which examines bacterial genes to understand resistance mechanisms. Conducted between March 2022 and March 2024, the study analysed 447 wastewater samples collected from Delhi, Mumbai, Kolkata, and Chennai.

The findings published in ‘Nature Communications’ reveal a complex picture. While different bacterial species dominate in different cities, they rely on similar genetic strategies to resist antibiotics. Bacteria develop resistance through specific genes that may strengthen their cell walls to block antibiotic entry, help expel or metabolise antibiotic molecules, or even destroy the drugs.

Importantly, bacteria can share these resistance genes not only with their offspring but also with neighbouring bacteria. The study found that microbial communities varied based on local environmental conditions. For instance, Klebsiella pneumoniae was more abundant in Chennai and Mumbai, while Pseudomonas aeruginosa was more prevalent in Kolkata. Despite these differences, resistance genes against multiple antibiotics were largely consistent across all four cities.

Antibiotics belong to different chemical classes, such as tetracyclines, beta-lactams, and macrolides. The researchers found that resistance genes against tetracyclines and beta-lactams are shared far more easily among bacteria than those against macrolides. Beyond identifying the threat, the researchers advocate expanding wastewater-based pathogen surveillance across the country.

“We have developed and validated a standard operating procedure that allows effective sample storage at 4°C for up to seven days without compromising data quality. Samples can be sent to common testing hubs, making the approach suitable for resource-limited settings. Broader participation in wastewater surveillance will help detect early outbreaks and track the spread of drug-resistant pathogens in real time,” said Director, CSIR-CCMB, Vinay K. Nandicoori.