Hyderabad’s open drains reveal alarming levels of antibiotic resistance

Antibiotic‑resistant bacteria capable of infecting humans, livestock and animals are widespread in Hyderabad’s environment, according to a wastewater study that traced the city’s growing Anti-Microbial Resistance (AMR) problem to rampant antibiotic misuse.

Scientists from the Centre for Cellular and Molecular Biology (CCMB), in collaboration with the Tata Institute for Genetics & Society (TIGS), Bengaluru, and the Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, carried out the study using samples collected a couple of years ago from 10 open drains, four rivers and three lakes. All sampled sites receive untreated sewage from households, industries and farming activities.

The researchers identified 13 unique resistance mechanisms across 17 sampling locations, pointing to widespread antibiotic resistance in environmental bacterial communities. Gaining access to Sewage Treatment Plants (STPs) proved difficult due to the lack of official permissions, prompting the team to rely on open drains. They found that open drainage systems in large cities offer an unbiased snapshot of AMR patterns circulating in the environment.

These bacterial communities have the potential to infect a wide range of hosts, including humans, livestock, birds and animals. Using a culture-independent metagenomics approach, the scientists analysed samples from open drains across the twin cities and found that all pathogens listed in the India priority pathogen list — developed by the World Health Organisation (WHO) country office in collaboration with the Department of Biotechnology — were present in the city’s wastewater, except Haemophilus influenzae.

The WHO classifies antibiotic-resistant priority pathogens into critical, high and medium categories based on the severity of the threat they pose. The findings show that several major pathogens are evolving or acquiring antibiotic resistance genes to evade drugs across multiple antibiotic classes and hosts. AMR patterns were broadly similar across geographic locations within the city, reflecting the widespread and indiscriminate use of common antibiotics among the population.

Analysis of 89 unique Antibiotic Resistance Genes (ARGs) revealed high resistance to macrolides, followed by aminoglycosides, tetracyclines and beta-lactams. Resistance was detected across 72 drug classes, including aminoglycoside, macrolide, tetracycline, fluoroquinolone, elfamycin and lincosamide antibiotics.

Among the detected pathogens, Helicobacter pylori recorded the highest normalised read count, followed by Campylobacter jejuni, Escherichia coli, Neisseria gonorrhoeae and Neisseria meningitidis. Except at one site, all locations showed the presence of these five pathogens, which together accounted for 55.1% of total pathogen reads.

The researchers suggested that studying seasonal variations could help provide deeper insights into the AMR landscape. They also highlighted the potential of open-drain sampling as an effective surveillance model for semi-urban and rural areas that lack organised sewerage systems and STPs.

“The problem is widespread across the country, and subsequent studies in many cities have shown similarly alarming AMR levels in both large and small urban centres,” said TIGS Director and former CSIR-CCMB Director Rakesh Mishra. “Samples from open drainage sites provide a comprehensive picture of environmental AMR, as the waste includes inputs from humans, animals, industries, poultry and farming practices,” he added.

The study, published in the journal Environmental Research last year, underscores the urgency of tackling antimicrobial resistance not only in healthcare settings but also in shared environments.