A Virus Found in Wastewater Beat Back a Woman’s ‘Zombie’ Bacteria

For years, a type of bacteria called Enterococcus faecium lurked in Lynn Cole’s bloodstream. Often found in hospitals, E. faecium is usually a gut-dwelling bacteria but can creep into other areas of the body. Her doctors tried various antibiotics, but the bacteria was zombie-like: It kept coming back.

Running out of options after a month-long hospitalization in 2020, Cole and her family agreed to try an experimental treatment called phage therapy. Phages aren’t drugs in the traditional sense. They are tiny, naturally occurring viruses that selectively kill bacteria. Highly specific to the bacteria they attack, phages are showing promise against hard-to-treat infections when antibiotics fail.

Phage therapy is not yet approved in the US, UK, or Western Europe but is used regularly in Georgia, Poland, and Russia. Several clinical trials are underway to confirm its safety and test its efficacy. But to treat Cole, researchers at the University of Pittsburgh School of Medicine first needed to find a phage that would work against her particular bacterial strain.

Phages live in places where bacteria live, which is to say, everywhere. “We have found that a good place to look for phages is in environments where the bacteria you want to target are abundant,” says Daria Van Tyne, assistant professor of infectious diseases at Pitt and an author on a study about Cole’s case that was published today in the journal mBio.

So Van Tyne and her team looked to a source that’s teeming with gut bacteria: wastewater. They screened dozens of phages they had isolated from wastewater samples, but couldn’t find a match. So they reached out to colleagues at the University of Colorado for help.

“The thing about phages is that they’re very much the perfect example of precision medicine, because they are so exquisitely specific to a bacterium,” says Breck Duerkop, an associate professor of immunology and microbiology at the University of Colorado Anschutz School of Medicine and an author on the study.

Phages recognize and attach to certain receptors on the surface of bacteria. After entering a bacterial cell, they make copies of themselves and disrupt the bacteria’s normal function, causing the cell to burst.

Van Tyne’s team mailed a sample of Cole’s bacteria to Duerkop’s lab, which had been studying phages that interact with E. faecium. Duerkop’s group tested the sample against phages they had also fished out of wastewater and found one that they thought would target the bacteria. They sent the phage to Pittsburgh, where Van Tyne and her team prepared it to give to Cole.

Since phages are viruses, they need a host in order to replicate. That means they have to be grown inside cultivated samples of the bacteria they infect. Bacteria grow quickly in the lab, but the phages have to be removed, purified, and then tested to make sure they’re safe for patients to receive. The whole process of making a suitable phage therapy can take weeks or even months from the time a lab gets a request.