Doctors Combined Phage Therapy With Fecal Transplants to Fight Recurrent UTIs
Three women with years of recurrent UTIs tried an experimental combination: bacteriophage therapy to kill the E. coli in the bladder, and for two of them, a fecal microbiota transplant to clear the same bacteria from the gut. The case series is small, but it points at recurrent UTI as a gut reservoir problem, not just a bladder one.
Recurrent urinary tract infections are more than an inconvenience. Some women cycle through years of antibiotics, one flare-up after another, without ever getting free of the bacteria driving it. A growing body of research points to the gut as the real source of the problem, a reservoir where E. coli hides out between bladder infections and reseeds them. A new case series from Swiss and German hospital teams tried something different: pairing a virus that kills bacteria with a gut microbiome transplant, aiming at the bladder and the intestinal reservoir at the same time. The results, in three women with years-long recurrent UTI, are early and small, but they open a genuinely new angle on a stubborn problem.
Key takeaways
- Three women with long-standing recurrent UTI (5 to 44 years of infections) received an 8-day bacteriophage therapy protocol; two of them also received a fecal microbiota transplant afterward.
- The combination reduced or eliminated UTI episodes over 24 months of follow-up for two patients, though none of the three had the bacteria fully cleared from their body.
- This is a case series of just three people, not a controlled trial. It does not prove the combination works broadly, only that it is worth testing in a real randomized trial.
- The treatment was well tolerated, with no adverse effects and stable kidney and liver function throughout.
Phage Therapy Plus Fecal Transplants Targeted the Gut Reservoir Behind UTIs
Researchers at Balgrist University Hospital in Zurich and Cologne University Hospital in Germany combined bacteriophage therapy (a treatment that uses viruses which infect and kill specific bacteria) with faecal microbiota transplantation (FMT, a procedure that transfers processed stool from a healthy donor to help recolonize a patient's gut) to attack the E. coli behind recurrent urinary tract infections (rUTI) from two directions at once. All three patients received an 8-day course of a two-phage cocktail, taken orally and then instilled directly into the bladder (intravesical, or IVS, administration) through a catheter. Two of the three patients went on to receive FMT by capsule about four days after finishing the phage course, following a short course of an additional antibiotic to prepare the gut. The logic, as the authors describe it, is that E. coli is not just a bladder problem: it persists as a reservoir in the gut, reseeding the bladder even after treatment, so clearing the gut may be necessary to break the cycle.
Recurrent UTI Drains Quality of Life and Drives Heavy Antibiotic Use
Recurrent UTI, defined clinically as two infections within six months or three within a year (see the CDC's overview of UTI management for the diagnostic criteria doctors use), is a genuinely common problem. The study's authors cite it as a leading cause of outpatient antibiotic prescribing, responsible for more than 15% of all such prescriptions. The three women in this case series were well outside the typical case, though: they had lived with recurrent infections for between 5 and 44 years, and each had needed 4 to 10 rounds of antibiotics in the year before the study alone. That kind of repeated antibiotic exposure is exactly the sort of pressure that reshapes the gut microbiome over time and can select for more resistant bacteria, part of why researchers are looking past antibiotics alone for a fix.
Three Patients, One 8-Day Phage Protocol, Two Received FMT
The study is a case series, the clinical term for a detailed writeup of what happened to a specific, small group of patients, not a randomized trial. All three participants were women between 20 and 70 years old with confirmed E. coli infections that had resisted a wide range of prior treatments. The phage cocktail used two wild-type E. coli viruses, named E2 and phi41S, isolated from wastewater in Switzerland. Patients took it orally for the first two days, then added twice-daily bladder instillations through day 8, followed by a short course of the antibiotic co-trimoxazole. Two patients then took a pretreatment antibiotic (vancomycin) before receiving FMT, delivered as 30 capsules made from a single donor's stool by the Cologne Microbiota Bank. The third patient did not receive FMT. All three were followed for up to 24 months afterward.
What the Combination Actually Did for Each Patient
The honest answer to whether this worked depends on which patient. Patient 1, who received both phage therapy and FMT, had fewer UTI episodes, reported less severe symptoms, and needed no further antibiotic treatment during follow-up. Patient 2, also treated with both, had no further UTI episodes at all during the 24-month follow-up, the strongest result in the series, though whole-genome sequencing showed her original E. coli strain was actually replaced partway through treatment by a different, less aggressive strain that has not caused a new infection since. Patient 3, who received phage therapy alone without FMT, self-reported less severe symptoms and fewer antibiotic courses, but did not see a drop in how often symptoms occurred. Across all three, phage reached the bladder fast: pathogen counts dropped by 3 log10 (roughly a thousandfold) within two hours of the first bladder instillation, and two patients saw counts fall by a full 7 log10 (about ten-million-fold) at their lowest point.
E. coli Was Never Fully Cleared, and the Sample Is Tiny
No, this study does not show the treatment eliminated the bacteria. E. coli was detected again in follow-up urine, vaginal, or stool samples from all three patients within the 30-day monitoring window, even after the additional antibiotic course. The authors are upfront that a case series of three patients, without a comparison group or blinding, cannot prove cause and effect: symptoms could have eased for reasons unrelated to the treatment, and because only two of the three patients received FMT, the study cannot separate what the phage therapy did from what the fecal transplant added on top of it. Much of the reported improvement in symptom severity and quality of life came from the patients themselves, a weaker form of evidence than an objective clinical measure.
Larger Randomized Trials Are Already Underway
The natural next step is exactly the kind of trial this case series cannot be: a randomized controlled trial with a comparison group and enough patients to separate a real effect from chance. The authors note that the only completed phase 2 randomized trial of phage therapy for UTI, run in patients undergoing prostate surgery, found phage non-inferior to antibiotics but not superior to placebo, a reminder that promising case reports do not always survive rigorous testing (see the trial's findings). A separate ongoing phase 2 trial testing a genetically enhanced phage cocktail alongside oral antibiotics for uncomplicated E. coli UTI has already reported encouraging early safety and pharmacokinetic data (see the ELIMINATE trial results). FMT itself has a longer track record against drug-resistant gut bacteria more broadly. A 2019 systematic review found it can reduce carriage of multidrug-resistant organisms, though results are inconsistent across studies. Until a dedicated randomized trial of this specific phage-plus-FMT combination is completed, this remains a documented, promising first attempt, not a treatment ready for clinical use.
Common Questions
Is this combination of phage therapy and FMT available to patients now?
No. This was an experimental treatment given to three patients as individual attempts at two hospitals in Switzerland and Germany, not an approved therapy, and it has not been tested in a randomized clinical trial.
What is fecal microbiota transplantation, and is it safe?
FMT transfers processed stool from a screened, healthy donor into a patient's gut, usually to restore a more typical mix of gut bacteria. In this study it was delivered as oral capsules and was well tolerated, with no adverse effects reported, though FMT products in general carry a small risk of transmitting infection if donor screening misses something.
Why would a gut treatment help a bladder infection?
Because recurrent E. coli UTI is increasingly understood as a reservoir problem. The same bacterial strain can persist in the gut and reintroduce itself into the bladder even after a bladder infection clears, so treating the bladder alone may leave the source untouched.
Did the treatment cure the infections?
Not consistently. One of the three patients had no further UTI episodes over 24 months, one had fewer and milder episodes but still needed antibiotics, and one saw no change in how often infections occurred. E. coli was still detected in follow-up samples from all three.
Evidence Rating
EMERGING — 61/100
Caveats
- This is a case series of only three patients treated by one team at two hospitals, not a randomized trial, so results cannot be generalized to how recurrent UTI patients would respond on average.
- There was no control group or blinding, and only two of the three patients received the fecal transplant, so the study cannot separate the effect of phage therapy from the effect of FMT.
- E. coli was detected in follow-up samples from all three patients, meaning the treatment did not fully eradicate the bacteria; in one patient, the original strain was replaced by a different, less virulent strain, which the authors say underscores the need for strain-level evaluation.
- Outcomes were largely self-reported (symptom severity, quality of life, antibiotic use) rather than confirmed by an independent objective measure, and there is no completed randomized trial yet showing this specific combination works.
This is a case series of three patients, not a controlled trial, so it describes what happened in these specific individuals rather than what would happen on average across a broader population. All three received an 8-day course of oral and intravesical two-phage therapy; two also received fecal microbiota transplantation afterward. Outcomes were tracked, and largely self-reported, for up to 24 months, with no control group, randomization, or blinding, so the study cannot attribute improvement specifically to the phage therapy, the FMT, or their combination. E. coli was never fully eradicated in any patient, and in one case the original strain was replaced by a different strain rather than cleared. The authors themselves frame this as a rationale-building first experience that should be followed by a randomized controlled trial, not as proof the combination treats recurrent UTI.
References
- Shawna McCallin, Annika Y. Classen, Simone C. Lieberknecht-Jouy, et al. (2026). Combined phage therapy and faecal microbiota transplantation to treat recurrent urinary tract infection: a case series. Nature Microbiology. https://doi.org/10.1038/s41564-026-02409-0
- Urinary Tract Infections: Clinical Overview | CDC. cdc.gov. https://www.cdc.gov/uti/hcp/clinical-overview/index.html
- Safety, pharmacokinetics, and pharmacodynamics of LBP-EC01, a CRISPR-Cas3-enhanced bacteriophage cocktail, in uncomplicated urinary tract infections due to Escherichia coli (ELIMINATE). NIH. https://pubmed.ncbi.nlm.nih.gov/39134085/
- S. Saha, R. Tariq, P.K. Tosh, D.S. Pardi, S. Khanna (2019). Faecal microbiota transplantation for eradicating carriage of multidrug-resistant organisms: a systematic review. Clinical Microbiology and Infection. https://doi.org/10.1016/j.cmi.2019.04.006
