Every 15 minutes, someone in the U.S. dies of a drug-resistant superbug . A few decades from now, antibiotic-resistant bacterial infections threaten to become the leading cause of death worldwide , outpacing cancer.
In the race for a solution to the antibiotic resistance crisis, a century-old practice is attracting renewed interest. The treatment, called phage therapy, involves co-opting friendly viruses that kill bacteria but ignore human cells.
Bacteria can — and do — develop resistance to phages, just as they do with antibiotics. But unlike antibiotics, phages can evolve counter defenses of their own.
Now, researchers at Michigan State University have identified a counter defense used by a group of phages common in the human gut, called Enterobacteria phage T2, that helps them stay one step ahead of their bacterial hosts.
These phages have mutation hotspots scattered throughout their genomes that help them modify key defense genes, the researchers report.
In a study published Aug. 13 in the journal Nature Microbiology, they show that these mutation hotspots help diversify their progeny to employ different survival strategies, ensuring that at least some continue to infect and kill no matter what countermeasures their bacterial hosts throw at them.
"They're essentially hedging their bets," said co-author Chris Waters , a core faculty member in MSU's Ecology, Evolution, and Behavior program.
"If we can harness these kinds of evolutionary tricks, we might be able to make more effective phage therapies in response to the antibiotic resistance crisis," Waters added.
The idea of using phages in medicine isn't new. Cocktails of phages have been used since the 1920s to treat dysentery, sepsis, pneumonia and other ailments, particularly in France, Poland and parts of the former Soviet Union.
Interest in phage therapy waned in the West after the discovery of penicillin and other chemical antibiotics in the 1940s. But now, with deadly microbes from MRSA to tuberculosis becoming resistant to more and more of these drugs, researchers are revisiting phage therapy to combat antibiotic-resistant infections.
When phages invade, they latch onto a bacterium and inject their genes into the cell. Once inside, they hijack the bacterium's internal machinery and turn it into a virus factory, forcing their host to churn out new phages until the cell bursts and releases them.
To fend off these attacks, bacteria have their own tactics. The researchers were studying one such strategy — a system in the bacterium that causes cholera — when they noticed something odd. In previous work, they identified a set of genes in cholera that spot the DNA of invading phages and chop it up before the phages can take over. But interestingly, this anti-virus protection didn't last for long.
First author Jasper Gomez conducted the work while earning his Ph.D. in the Waters lab in MSU's department of microbiology, genetics, & immunology.
In their experiments, the researchers transferred cholera DNA encoding the protective system to E. coli, a bacterium that is easier to work with in the lab, and exposed the bacteria to phages. Before long, the engineered E. coli were under attack. In other words, the phages quickly devised a workaround to bypass their hosts' defenses, allowing them to sneak in and hijack their victims' cells anyway.
"Within a few hours, the phages always started to win," Waters said. "We couldn't understand why," he added.
The researchers sequenced the DNA of the resistant phages and found that many had "typos" in a gene called agt, particularly in a region of repetitive DNA where the same letter, or nucleotide base, appeared multiple times in the gene sequence.
"When I saw the data, I thought, oh my gosh," Waters said. The region resembled a type of mutational hotspot called a contingency locus. Well studied in other organisms but never shown in phages before, such regions of the genome are known to be places where the cell's DNA copying machinery sometimes "slips" and makes mistakes, Waters said.
The result is that, each time new phages are produced, they aren't producing exact genetic copies of their ancestor. Some of the resistant mutants gain an extra repeat unit in the agt gene, while others lose one, throwing off how the gene's instructions are read.
The researchers found that the repetitive region accumulates mutations thousands of times faster than the rest of the genome.
While mutations are often harmful, this changeability can give phages an evolutionary edge, Waters said. By continually churning out new mutants, they increase the odds that at least some will carry a mutation that lets them evade or disarm their host's ever-changing arsenal.
"This changes our understanding of how phages evolve," Waters said. "Instead of hijacking their hosts to mass produce exact copies of themselves, they are actually using these mutation hotspots to make a zoo."
Phages outnumber bacteria by around ten to one, making them the most abundant organisms on the planet. The researchers focused on a type of phage that lurks in the gut, where it specializes on E. coli bacteria, but phages can be found just about anywhere, from the sands of the Sahara Desert to the ice of the Arctic Sea.
Working with MSU microbial evolution expert Jeffrey Barrick , the team found hundreds of similar mutation hotspots scattered across the genomes of other phage species as well.
Next, the researchers are looking into whether these mutation hotspots give phages an edge in other situations, such as adapting to survive and exploit their bacterial hosts after a shift in the environment, or evolving to infect new types of bacteria.
In much of the U.S. , the U.K., and elsewhere, phage therapy is still far from mainstream; regulatory hurdles make it available only as a last resort. In the meantime, Waters and other researchers at MSU are exploring potential applications beyond the clinic, to treat bacterial infections in everything from honeybees and crops to pets and livestock.
"MSU could be a great phage therapy center for veterinary and agriculture applications," Waters said.
"We're never going to be able to completely get rid of resistance," he added. "But if we can better understand how bacteria protect themselves from phage infection and how phages fight back, we might be able to minimize it."
This research was supported by grants from the U.S. National Institutes of Health (GM139537, AI158433, GM088344 and F31AI186463) and the National Science Foundation (DEB-1813069 and DEB-1951307).
CITATION: "Phage-encoded contingency loci enable bet-hedging against host defence mechanisms," Jasper B. Gomez, Jeffrey E. Barrick, Christopher M. Waters. Nature Microbiology, Aug. 13, 2026. DOI: 10.1038/s41564-026-02445-w
