A new study has found that COVID-19 infection may be doing more than causing a viral illness – it could also be helping antibiotic-resistant bacteria gain a foothold in the upper airways, potentially making secondary bacterial infections harder to treat.

The research, published in the journal Current Microbiology, found that people infected with SARS-CoV-2 carried significantly higher levels of antibiotic resistance genes in their noses and throats than people who did not have COVID-19.

These resistance genes were linked to bacteria such as Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus – organisms that are commonly responsible for serious secondary infections, including urinary tract infections, acute diarrhoea, pneumonia, neonatal meningitis and even sepsis, many of which can be life-threatening.

The findings do not mean COVID-19 directly creates antibiotic resistance. Rather, the infection appears to change the microbial environment in the respiratory tract in a way that favours bacteria carrying resistance genes.

In other words, the findings highlight that viral infections can influence not only the body's immune response but also the microbial communities that live alongside us, with consequences that may outlast the infection itself.

Estimates suggest that in 2021, around 10.7 lakh Indians were infected with deadly, drug-resistant bacteria or superbugs.

Also, between 3 lakh and 10.4 lakh deaths in India in 2019 were linked to bacterial antimicrobial resistance (AMR), according to a global report by the GRAM (Global Research on Antimicrobial Resistance) Project.

COVID TURNING BACTERIA INTO SUPERBUGS

Researchers analysed 95 upper respiratory tract samples collected in central India using shotgun metagenomic sequencing, a technique that identifies the genetic material of all microbes present in a sample. They found that 21 of the 22 antibiotic resistance genes that differed significantly between the two groups were more abundant in people with COVID-19.

The study also found that the viral infection itself – not factors such as age or where people lived – was the strongest factor associated with these changes.

Dr Krishna Khairnar, scientist and head of environmental epidemiology and pandemic management at the Council of Scientific and Industrial Research – National Environmental Engineering Research Institute (CSIR-NEERI), and a co-author of the study, said mapping the "resistome" – the collection of antibiotic resistance genes -in COVID-19 patients is a relatively new area of research.

"The findings demonstrate distinct SARS-CoV-2-associated alterations in the upper respiratory tract resistome, with enrichment of multiple antimicrobial resistance genes linked to opportunistic bacterial pathogens, including Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus," said Dr Khairnar.

The division he heads at NEERI is also a World Health Organisation- Coronavirus Network (WHO-CoViNet) reference laboratory.

In simple terms, every person naturally carries bacteria in the nose and throat and most of these bacteria are harmless and coexist with us without causing illness.

But the new study suggests that during COVID-19, these bacterial communities become enriched with genes that help them survive antibiotic treatment. If these bacteria later cause an infection, doctors could find it more difficult to treat them with standard antibiotics.

Dr Khairnar also said the work improves understanding of the relationship between viral infections and antimicrobial resistance and underlines the importance of metagenomic surveillance in shaping public health strategies.

WHY THE FINDINGS MATTER

Some experts not involved in the research say the findings are important but should be interpreted carefully.

Dr Rajeev Jayadevan, a Kerala-based clinician and medical researcher, told India Today the study looked at bacteria that normally live in the nose and throat and compared COVID-positive patients with healthy people who did not have symptoms.

"Essentially, the study says that bacteria that naturally live in the respiratory tract display more resistance during an active respiratory illness," he said.

He explained that the human body normally hosts numerous bacteria, many of which do not cause disease. However, viral infections and antibiotic use can alter this balance.

When antibiotics are taken, susceptible bacteria die while resistant ones survive and multiply, increasing the proportion of bacteria carrying resistance genes.

Dr Jayadevan cautioned that the study did not examine whether participants had previously taken antibiotics, which could also explain the higher levels of resistance genes. "It could be either because these individuals may have taken prior antibiotic courses – which the study did not look at – or it could be related to the illness itself," he said.

He added that similar patterns have been observed with respiratory illnesses even before the COVID-19 pandemic, making it unlikely that the virus alone directly causes antibiotic resistance.

Even so, the findings raise concerns because secondary bacterial infections remain a major cause of complications in patients recovering from viral illnesses. If the bacteria already present in the airways carry more resistance genes, infections that develop later could become harder to treat, increasing the need for stronger antibiotics.

The study did not track whether participants actually developed bacterial infections. Instead, it mapped the "resistome", the pool of resistance genes present in the microbial community.

Still, researchers say this provides an important early warning because it shows that COVID-19 may create conditions that favour bacteria equipped with a stronger arsenal against antibiotics.

At a time when AMR is recognised as one of the world's biggest public health threats, the findings add another reason to use antibiotics judiciously and strengthen surveillance of resistant bacteria.

- Ends

Published On:

Jul 21, 2026 15:55 IST