A three-patient case series from Zurich and Cologne combined bacteria-killing viruses with fecal microbiota transplantation to clear E. coli from the bladder and gut, setting up a clinical trial planned for 2027.

For many women, a urinary tract infection is not a one-time misery. Recurrent infections can return again and again, each treated with another round of antibiotics. Over time, the bacteria behind them can become resistant, leaving fewer options that work.

Researchers in Switzerland and Germany now report an alternative approach that combines two unconventional treatments. In a case series published in Nature Microbiology, they describe treating three women with antibiotic-resistant recurrent urinary tract infections using bacteriophages, viruses that kill bacteria, followed in two cases by a fecal microbiota transplant. According to the release, it is the first time the two approaches have been combined to clear infection reservoirs in both the urinary tract and the gut.

A common and stubborn problem

Urinary tract infections are among the most common bacterial infections, and they mostly affect women. A substantial share of women who have one will have another, and some develop recurrent infections that return several times a year.

Most are caused by Escherichia coli. The bacteria that infect the bladder often originate in the gut, which is one reason infections keep coming back: even if an infection is cleared from the urinary tract, a reservoir of the same bacteria can remain in the intestines.

Antibiotics are the standard treatment, but repeated courses drive resistance. The World Health Organization has identified antimicrobial resistance as one of the top global public health threats.

Viruses that hunt bacteria

Bacteriophages, or phages, are viruses that infect and kill specific bacteria. They were discovered more than a century ago and were used to treat infections before the antibiotic era, particularly in the former Soviet Union and Eastern Europe, where phage therapy has continued. Elsewhere, antibiotics largely displaced them.

Interest in phages has revived as antibiotic resistance has grown. Because phages are highly specific, they can target a particular pathogen while leaving most of the body’s other bacteria alone.

Fecal microbiota transplantation, or FMT, involves transferring stool from a healthy donor into a patient’s gut to restore a healthy community of microbes. It is already an established treatment for recurrent infections with the bacterium Clostridioides difficile.

Treating the bladder and the gut

The project was led by Shawna McCallin and Lorenz Leitner of Balgrist University Hospital in Zurich, with Lena Biehl and Annika Y. Classen of University Hospital Cologne and Maria Vehreschild of Goethe University Frankfurt. The German Center for Infection Research (DZIF) supported the analysis of samples.

Between May and July 2023, three women with recurrent urinary tract infections caused by E. coli that had not responded to antibiotics were treated at Balgrist. All three received eight days of phage therapy, given both by mouth and directly into the bladder. Two then received FMT in Cologne to target E. coli in the gut.

“While phage therapy acts to remove the pathogen, FMT aims to restore a healthy microbiome, combining both immediate and long-term effects,” Biehl said.

Phage treatments are usually tailored to the patient. Because each phage infects only certain strains of a bacterium, clinicians typically test a patient’s bacteria against a library of phages to find ones that will work, a personalized approach that differs from the one-size-fits-all model of most antibiotics.

Lasting relief in two patients

No noticeable side effects occurred. The two women who received both treatments had a sustained reduction in urinary tract infections over two years. The woman who received phage therapy alone had further infections, although with milder symptoms.

All three reported a much better quality of life and far less use of antibiotics.

Next, a clinical trial

The researchers are clear about the limits of their results. “Three patients are not a sufficiently large sample to establish this new therapy, and control groups were lacking,” McCallin said.

Without a comparison group, it is impossible to know how much of the improvement was due to the treatments rather than to chance or to other factors. Case series like this one are typically used to show that an approach is safe and worth testing properly.

That is the next step. A clinical trial is scheduled to begin in June 2027 at the participating institutions as part of the REPhRAME project, funded by the European Commission’s Horizon Europe program.

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Notes

1. “Combined Phage therapy and fecal microbiota transplantation to treat recurrent urinary tract infection: a case series.” Nature Microbiology, 2026. DOI: 10.1038/s41564-026-02409-0.
2. University of Cologne. “Thinking beyond antibiotics in the treatment of urinary tract infections.” EurekAlert!, 30 July 2026. https://www.eurekalert.org/news-releases/1138218.