How viruses can help the fight against antibiotic resistance

India Today

13-06-2025

Phage therapies are currently used only in compassionate cases, where all antibiotics have failed and the patient's condition is critical. () Phage therapy uses viruses that specifically infect bacteria
India currently relies mostly on antibiotics for infections
AI helps identify and analyse over 1.3 million viral genomes
Antimicrobial resistance isn't just a silent pandemic â€' India bears one of the heaviest burdens globally.
While the country continues its search for new antibiotics to combat the crisis, researchers are now turning to naturally-occurring viruses in the environment as a promising tool to attack and kill multi-drug-resistant bacteria.
Karthik Anantharaman, a visiting professor at Wadhwani School of Data Science and AI at IIT Madras, is spearheading such a project in the US by studying the nature of viruses in their natural habitat to attack and kill bacteria, a process called phage therapy.
"One approach is to create more antibiotics but this only postpones the problem. New antibiotics also can lead to new forms of resistance, creating a never-ending cycle. An alternative and promising solution is phage therapy, which uses viruses called bacteriophages (or simply phages) to kill specific bacteria," Dr. Anantharaman, who is also a professor at the University of Wisconsin-Madison, told IndiaToday.in.
FINDING VIRUSES THAT KILL BACTERIA
Anantharaman and his team discovered that viruses have yearly cycles and can affect other organisms in the ecosystem.
As part of their study, some viruses were found to carry genes they had taken from the organisms they infected, which helped them carry out important biological functions.
The research team also put together over 1.3 million viral genomes â€' the largest collection of its kind so far. Lake Mendota in the US has been monitored consistently since the late 1800s (Photo: Center for Limnology, University of Wisconsin–Madison)
"In our lab, we are exploring how phages behave over time. We conducted a 20-year study of a single lake, using DNA sequencing and artificial intelligence (AI) to track how phage populations changed. By sequencing environmental DNA and using AI tools, we identified over 1.3 million viral genomes. This allowed us to see how viruses shift month to month, season to season, and year to year, and to predict their future behaviour," Dr. Anantharaman said.
While phage therapy might seem like a relatively new concept to Indian populations and even the West who rely heavily on antibiotics, Anantharaman mentioned that the phenomenon of using viruses to kill bacteria has been used in countries like Russia, Poland, Ukraine, and Georgia for decades.
VIRUSES AS ENVIRONMENTAL CLEANER
"Our goal is twofold: to improve human health and environmental health. Just as phages (virus) can target harmful bacteria in the human body, they can also be used to clean polluted ecosystems," University of Wisconsin-Madison professor said.
For example, if a lake turns black or emits a smell like rotten eggs, a sign of hydrogen sulfide produced by bacteria, phages can be used to selectively kill those bacteria and restore the lake's health. Anantharaman lab group at the University of Wisconsin-Madison, US, pictured by Lake Mendota.
Despite their promise, phage therapies are currently used only in compassionate cases, where all antibiotics have failed and the patient's condition is critical.
HOW DO PHAGES OR VIRUSES WORK AGAINST BACTERIA?
One major reason phages haven't entered mainstream treatment is that researchers still don't fully understand how they evolve over time.
Consequently, there are no approved phage-based therapeutic products in India, the US, or Europe.
But phages hold great promise, especially when used in combination with antibiotics.
Here's how it works: when bacteria face antibiotics, they come under stress. Sometimes, this stress causes genetic changes that make them resistant.
But in that process, bacteria may also become vulnerable to phages. So, using both antibiotics and phages together creates a powerful, complementary treatment strategy.
In some cases, antibiotics work where phages don't and vice versa. Anantharaman lab member Patricia Tran sampling Lake Mendota, US. over frozen ice in the Winter.
"One major advantage of phages is their precision. Unlike antibiotics, which kill both harmful and beneficial bacteria, phages target only one specific strain. If a person is infected with Pseudomonas, the phage used will kill only Pseudomonas, sparing the rest of the body's microbiome. That's a game-changer for preserving overall health during treatment," Anantharaman explained.
Another surprising fact is that viruses are everywhere - even inside us.
There are 10 to 100 times more viral particles in and on our bodies than human cells.
These include many harmless phages that silently regulate bacterial populations. Phages are found in lakes, rivers, soil, oceans, and even in our intestines and on our skin. Anantharaman lab member Dinesh Kumar Kuppa Baskaran sampling Lake Mendota in the Summer.
"In our lab, we use AI â€' both machine learning and deep learning â€' to rapidly identify phages from environmental samples. This process, which used to take years, now takes just a day. AI allows us to sift through millions of DNA sequences and pinpoint the viruses that can infect specific harmful bacteria," Anantharaman said.
BARRIERS PERSIST
However, awareness remains a major barrier.
The medical community and industry are still focused on antibiotics. There's limited investment in phage therapy, and the necessary research infrastructure hasn't yet been built.
For phage therapy to move forward, government support and academic research are essential.
"Industry isn't currently interested in developing phage-based treatments â€' it's mostly up to institutions and public funding. But as the threat of antibiotic resistance grows, this is expected to change," Anantharaman opined.
Phage therapy isn't just a scientific curiosity. It could be a major pillar of future medicine â€' if we choose to invest in it.
Antimicrobial resistance isn't just a silent pandemic â€' India bears one of the heaviest burdens globally.
While the country continues its search for new antibiotics to combat the crisis, researchers are now turning to naturally-occurring viruses in the environment as a promising tool to attack and kill multi-drug-resistant bacteria.
Karthik Anantharaman, a visiting professor at Wadhwani School of Data Science and AI at IIT Madras, is spearheading such a project in the US by studying the nature of viruses in their natural habitat to attack and kill bacteria, a process called phage therapy.
"One approach is to create more antibiotics but this only postpones the problem. New antibiotics also can lead to new forms of resistance, creating a never-ending cycle. An alternative and promising solution is phage therapy, which uses viruses called bacteriophages (or simply phages) to kill specific bacteria," Dr. Anantharaman, who is also a professor at the University of Wisconsin-Madison, told IndiaToday.in.
FINDING VIRUSES THAT KILL BACTERIA
Anantharaman and his team discovered that viruses have yearly cycles and can affect other organisms in the ecosystem.
As part of their study, some viruses were found to carry genes they had taken from the organisms they infected, which helped them carry out important biological functions.
The research team also put together over 1.3 million viral genomes â€' the largest collection of its kind so far. Lake Mendota in the US has been monitored consistently since the late 1800s (Photo: Center for Limnology, University of Wisconsin–Madison)
"In our lab, we are exploring how phages behave over time. We conducted a 20-year study of a single lake, using DNA sequencing and artificial intelligence (AI) to track how phage populations changed. By sequencing environmental DNA and using AI tools, we identified over 1.3 million viral genomes. This allowed us to see how viruses shift month to month, season to season, and year to year, and to predict their future behaviour," Dr. Anantharaman said.
While phage therapy might seem like a relatively new concept to Indian populations and even the West who rely heavily on antibiotics, Anantharaman mentioned that the phenomenon of using viruses to kill bacteria has been used in countries like Russia, Poland, Ukraine, and Georgia for decades.
VIRUSES AS ENVIRONMENTAL CLEANER
"Our goal is twofold: to improve human health and environmental health. Just as phages (virus) can target harmful bacteria in the human body, they can also be used to clean polluted ecosystems," University of Wisconsin-Madison professor said.
For example, if a lake turns black or emits a smell like rotten eggs, a sign of hydrogen sulfide produced by bacteria, phages can be used to selectively kill those bacteria and restore the lake's health. Anantharaman lab group at the University of Wisconsin-Madison, US, pictured by Lake Mendota.
Despite their promise, phage therapies are currently used only in compassionate cases, where all antibiotics have failed and the patient's condition is critical.
HOW DO PHAGES OR VIRUSES WORK AGAINST BACTERIA?
One major reason phages haven't entered mainstream treatment is that researchers still don't fully understand how they evolve over time.
Consequently, there are no approved phage-based therapeutic products in India, the US, or Europe.
But phages hold great promise, especially when used in combination with antibiotics.
Here's how it works: when bacteria face antibiotics, they come under stress. Sometimes, this stress causes genetic changes that make them resistant.
But in that process, bacteria may also become vulnerable to phages. So, using both antibiotics and phages together creates a powerful, complementary treatment strategy.
In some cases, antibiotics work where phages don't and vice versa. Anantharaman lab member Patricia Tran sampling Lake Mendota, US. over frozen ice in the Winter.
"One major advantage of phages is their precision. Unlike antibiotics, which kill both harmful and beneficial bacteria, phages target only one specific strain. If a person is infected with Pseudomonas, the phage used will kill only Pseudomonas, sparing the rest of the body's microbiome. That's a game-changer for preserving overall health during treatment," Anantharaman explained.
Another surprising fact is that viruses are everywhere - even inside us.
There are 10 to 100 times more viral particles in and on our bodies than human cells.
These include many harmless phages that silently regulate bacterial populations. Phages are found in lakes, rivers, soil, oceans, and even in our intestines and on our skin. Anantharaman lab member Dinesh Kumar Kuppa Baskaran sampling Lake Mendota in the Summer.
"In our lab, we use AI â€' both machine learning and deep learning â€' to rapidly identify phages from environmental samples. This process, which used to take years, now takes just a day. AI allows us to sift through millions of DNA sequences and pinpoint the viruses that can infect specific harmful bacteria," Anantharaman said.
BARRIERS PERSIST
However, awareness remains a major barrier.
The medical community and industry are still focused on antibiotics. There's limited investment in phage therapy, and the necessary research infrastructure hasn't yet been built.
For phage therapy to move forward, government support and academic research are essential.
"Industry isn't currently interested in developing phage-based treatments â€' it's mostly up to institutions and public funding. But as the threat of antibiotic resistance grows, this is expected to change," Anantharaman opined.
Phage therapy isn't just a scientific curiosity. It could be a major pillar of future medicine â€' if we choose to invest in it. Join our WhatsApp Channel