Mutation hotspots help 'friendly' viruses outmaneuver the bacteria in your gut

Each day, approximately one person in the United States succumbs to a drug-resistant superbug. In a few decades, bacterial infections that resist antibiotics are anticipated to claim more lives than cancer. Antibiotic resistance is a growing concern, driving interest in an old technique known as phage therapy. This method entails utilizing harmless viruses to eliminate bacteria but spare human cells.

However, bacteria can develop resistance to phages, just as they do with antibiotics. Yet, unlike antibiotics, phages possess the ability to evolve counterdefenses. Scientists at Michigan State University have uncovered a specific defense mechanism employed by a group of phages prevalent in the human gut, referred to as Enterobacteria phage T2.

This defense enables them to remain one step ahead of their bacterial adversaries. The researchers published their findings on August 13 in the journal Nature Microbiology. As reported by co-author Chris Waters, these mutation hotspots enable the phages to diversify their descendants, equipping them with various survival tactics, ensuring that some continue to infect and kill even when the bacterial hosts employ countermeasures.

The concept of harnessing phages in medicine is not new. Since the 1920s, cocktails of phages have been used to treat dysentery, sepsis, pneumonia, and other ailments, mainly in France, Poland, and parts of the former Soviet Union. However, phage therapy fell out of favor in the West after the discovery of penicillin and other chemical antibiotics in the 1940s.

Recently, due to the emergence of lethal microbes like MRSA and tuberculosis becoming resistant to more and more of these drugs, researchers have again turned to phage therapy to combat antibiotic-resistant infections. When phages attack, they bind to a bacterium, inject their genes into the cell, and override the bacterium's internal machinery, turning it into a factory for producing new phages.

Eventually, the cell bursts and releases the phages. To counter these attacks, bacteria have their own strategies. During their research, scientists studying a defense mechanism in cholera bacteria noticed something unusual. They had previously identified a set of genes in cholera that detect invading phage DNA and destroy it before the phages can establish control.

However, they observed that this protective system did not last long. Jasper Gomez, the first author of the study, conducted the research while pursuing his Ph.D. in the Waters lab at MSU's Department of Microbiology, Genetics, & Immunology. In their experiments, Gomez transferred cholera DNA encoding the protective system to E. coli, a bacterium that is easier to work with in the lab, and subjected the bacteria to phages.

Within a few hours, the engineered E. coli were under siege. The phages swiftly devised a workaround to bypass their hosts' defenses, enabling them to infiltrate and hijack their victims' cells. Within a few hours, the phages consistently emerged victorious. The researchers sequenced the DNA of the resistant phages and discovered that many carried mutations in a gene called agt, particularly in a repetitive DNA region where the same letter, or nucleotide base, appeared multiple times in the gene sequence.

Waters was intrigued by the data and remarked, "Oh my gosh, this region resembled a type of mutational hotspot called a contingency locus." While such regions are well-studied in other organisms but never observed in phages before, they are known to be areas where the cell's DNA copying machinery occasionally makes mistakes. This results in each new phage generation producing genetic copies that are not exact replicas of their ancestors.

Some resistant mutants acquire an additional repeat unit in the agt gene, while others lose one, disrupting how the gene's instructions are read. These mutation hotspots accumulate mutations thousands of times faster than the rest of the genome. Although mutations are usually detrimental, this adaptability can provide phages with an evolutionary advantage.

By continuously generating new mutants, they increase the likelihood that some will carry a mutation that enables them to evade or neutralize their host's ever-changing arsenal. This finding challenges our understanding of how phages evolve. Instead of commandeering their hosts to mass-produce exact copies of themselves, phages utilize these mutation hotspots to create a diverse array of mutants.

Phages outnumber bacteria by roughly 10 to 1, making them the most abundant organisms on the planet. The researchers focused on a gut-specific phage that targets E. coli bacteria, but phages can be found in various environments, ranging from the Sahara Desert sands to the Arctic ice. Collaborating with MSU microbial evolution expert Jeffrey Barrick, the team identified hundreds of similar mutation hotspots scattered across the genomes of other phage species.

The researchers are now investigating whether these mutation hotspots provide phages with an advantage in other scenarios, such as adapting to survive and exploit their bacterial hosts after environmental shifts or evolving to infect new types of bacteria. Currently, phage therapy remains largely outside the mainstream in the U.S., the U.K., and other regions due to regulatory obstacles, and it is only accessible as a last resort.