New Delhi: Handrails, ticket kiosks and counters inside Chennai Metro stations carry distinct communities of microbes, including bacteria and genes associated with antibiotic resistance, according to a new study by researchers at the Indian Institute of Technology (IIT) Madras.
The study, published in the journal mSphere, analysed microbial DNA from surfaces across twelve Chennai Metro stations and trains. Researchers found genes linked to antibiotic resistance in more than 80 percent of the 41 samples analysed, although these genes were present in low amounts.
Antibiotic resistance occurs when bacteria develop the ability to survive medicines that would normally kill them or stop them from multiplying. This can make infections harder to treat and force doctors to use different, sometimes more expensive or less readily available medicines.
Bacteria can carry genes associated with antibiotic resistance. However, finding these genes on metro surfaces does not establish that passengers are at risk of infection. The study used DNA sequencing, which cannot distinguish between living and dead bacteria, and its findings do not establish whether the detected organisms could be transmitted or cause disease. The researchers compared Chennai’s microbial profile with data from other cities to identify patterns specific to the metro system.
The researchers describe the study as a foundation for understanding urban microbiomes in India. They say sustained monitoring could help track changes in microbial communities and inform targeted cleaning protocols and public health interventions.
“This was more of a proof-of-concept study, where we wanted to show that it is important to do these studies and understand these microbes,” Karthik Raman, professor in the Department of Data Science and AI at IIT Madras and one of the study’s co-authors, told ThePrint.
The research is part of the broader effort to map microbial communities in urban environments. The research is the first comprehensive study of the microbes found on surfaces in an Indian public transport system. Similar studies have been conducted in dozens of cities worldwide, Professor Raman said.
What studies in other countries have found
Several transit studies across the world have examined microbial communities found on public transport surfaces. The international Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) project, a global research consortium founded in 2015, studies the microbes living in cities by sampling metro systems and other public places. It wants to understand how these microbes differ from city to city and how geography and climate shape them.
In 2015, researchers at Weill Cornell tested surfaces across New York’s subway, parks and the Gowanus Canal. They found 1,688 types of microbes, and nearly half the DNA matched no known organism. The aim was to create a baseline to compare against in future. The project’s success led to the creation of the MetaSUB consortium later that year, which went on to sample cities worldwide.
A 2021 study in Cell tested 4,728 samples from metro systems in 60 cities over three years. Each city had its own microbial signature, linked to its climate and geography, and levels of antibiotic-resistance genes varied widely. MetaSUB has since expanded to air, water and sewage, and its wastewater work has won a $5 million grant linked to the US CDC’s wastewater surveillance system.
What the IIT Chennai study found
The findings of the Chennai metro study provide an initial reference point against which researchers can compare future samples and investigate whether the microbial communities on different surfaces change over time.
The IIT Madras team identified 72 families of genes associated with resistance to different antibiotics. Genes linked to resistance against antibiotics like rifamycins and sulfonamides were found in relatively higher amounts.
“We also found a lot of antibiotic resistance. This is still preliminary, because we have only sequenced it. It doesn’t mean these are actually going to show resistance,” Professor Raman said. This means the findings point to the presence of genetic sequences associated with antibiotic resistance, not confirmed antibiotic-resistant bacteria.
Professor Raman said the signatures give “a warning that we should be a little more careful”.
Nine species unusually common in Chennai
The researchers collected 96 samples in December 2021 and January 2022, during the Covid pandemic, by swabbing frequently touched surfaces such as handrails, ticket vending machines, station banisters and ticket counters. Of these, 47 passed the initial quality checks, while 41 had enough DNA sequencing data to be included in the final analysis.
They identified 30 “core” microbial species found in more than 97 percent of the analysed samples.
The team then compared its findings with data from 31 other cities. Nine species were found to be unusually common in Chennai, but were not commonly found at comparable levels in the other cities.
These bacteria are associated with different environments, including soil, water, air, poultry litter and, in one case, human skin. The researchers suggested that Chennai’s coastal location, warm climate and humidity could partly explain the presence of at least two bacteria strains.
Professor Raman said such comparisons show why these studies matter, since they reveal species that stand out in an Indian city. “We need to find out whether they have any health implications,” he said.
Researchers call for regular monitoring
Researchers have called for repeat sampling at the same locations across different seasons and over longer periods.
They would also need to use additional laboratory methods to establish whether the detected organisms are alive and whether resistance-associated genes are functional. This would help distinguish normal fluctuations in a city’s microbial environment from unusual changes that require further investigation.
Professor Raman said that routine monitoring could help researchers track changes in the microbes found in public spaces and identify unusual patterns during disease outbreaks.
He also argued that the goal should not be to make public spaces completely free of microbes. “I don’t think it’s possible to keep these places sterile, and that shouldn’t even be the goal,” he said. Instead, he suggested, future research could explore ways to encourage microbial communities dominated by less harmful organisms. The study itself, however, calls for targeted cleaning protocols for high-contact surfaces such as kiosks.
Such monitoring can be expensive, Professor Raman acknowledged, but he said it is necessary to build a clearer picture of India’s urban environment.
(Edited by Viny Mishra)