Combined Phage and Microbiota Therapy May Reduce Recurrent Urinary Tract Infections

They increase morbidity, expose patients to repeated antibiotic courses, and accelerate antimicrobial resistance. Persistent gut reservoirs that reseed the bladder make eradication difficult in many women. To help address this challenge, investigators have combined bacteriophage therapy with fecal microbiota transplantation for patients with difficult-to-treat rUTIs.

Researchers from University Hospital Balgrist and the University of Zurich, with collaborators at the University of Cologne, University Hospital Cologne, Goethe University Frankfurt, and the German Center for Infection Research (DZIF), evaluated a combined approach using phage therapy (PT) and fecal microbiota transplantation (FMT). The strategy was designed to decolonize both urinary and intestinal reservoirs in patients with recurrent infection. The case series was published in Nature Microbiology on July 30, 2026.

Phage therapy uses viruses that selectively target and destroy bacteria, including multidrug-resistant strains. In this program, three women with microbiologically confirmed Escherichia coli rUTIs that had not responded to antibiotics or common nonantibiotic strategies received PT outside acute episodes. Treatment lasted eight days and was delivered orally and intravesically via bladder catheter at Balgrist.

Two of the three patients then underwent elective FMT in Cologne to restore a healthier microbiome and address intestinal E. coli reservoirs that can persist after antibiotic treatment. All procedures were well tolerated with no noticeable side effects. Over two years of observation, the two patients who received both PT and FMT had a long-term reduction in urinary tract infections. The patient who received PT alone experienced additional episodes, but with reduced symptom severity.

Across all three cases, quality of life improved and the need for antibiotics decreased substantially. The experience is described as the first administration of PT together with FMT to decolonize urinary and intestinal reservoirs in rUTI. Treatments occurred between May and July 2023.

“Three patients are not a sufficiently large sample to establish this new therapy, and control groups were lacking. However, this experience has helped to lay the foundation for a clinical trial to test the clinical utility of this treatment approach and make it more widely available and sustainable for patients,” said Shawna McCallin, medical biologist at Balgrist University Hospital.

“While phage therapy acts to remove the pathogen, FMT aims to restore a healthy microbiome, combining both immediate and long-term effects,” said Lena Biehl, infectious disease researcher at University Hospital Cologne.

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Balgrist University Hospital
University Hospital Cologne