Fecal Putative Uropathogen Abundance and Antibiotic Resistance Gene Carriage in Women With Refractory Recurrent Urinary Tract Infection Treated With Fecal Microbiota Transplantation

Abstract

ObjectiveThe aims of this study were to describe the fecal relative abundance of potentially uropathogenic bacteria and to analyze antibiotic resistance genes before and after fecal microbiota transplantation in women with recurrent urinary tract infection (UTI).MethodsShotgun sequencing was performed on fecal samples from 3 donors and 4 women with recurrent UTI who underwent transplantation. Recipient samples were sequenced at baseline and at 4 time points through 6 months postintervention. Relative fecal uropathogen abundance was analyzed by species and participant using descriptive statistics. Antibiotic resistance gene abundance was assigned, normalized, and compared between donors and recipients at baseline and postintervention using an abundance bar plot, nonmetric multidimensional scaling, and pairwise permutational multivariate analysis of variance.ResultsThe median (range) relative abundance of Escherichia coli in all fecal samples from women with recurrent UTI was 0% (0%–5.10%); Enterococcus faecalis, 0% (0%–0.20%); Enterococcus faecium, 0% (0%–1.90%); Klebsiella pneumoniae, 0% (0%–0.10%); and Pseudomonas aeruginosa, 0% (0%–0.10%). Gut microbes carried genes conferring resistance to antibiotics used for UTI. No significant difference was seen in antibiotic resistance gene carriage after transplantation compared with baseline (P=0.22, R2=0.08 at 3 months). Antibiotic gene composition and abundance were significantly associated with the individual from whom the sample came (P=0.004, R2=0.78 at 3 months).ConclusionsExploratory analysis of gut microbiomes in women with recurrent UTI identifies no or low relative putative uropathogen abundance for all species examined. Antibiotic resistance gene carriage persisted after fecal microbiota transplantation, although conclusions are limited by small sample size.

Fecal Microbiota Transfer for Clostridium difficile Infection and Its Effects on Recurrent Urinary Tract Infection

“…In a retrospective study of FMT in patients with rUTI, the bacterial antibiotic susceptibility profile improved after FMT 5 . Comparatively, a recent study of patients having undergone FMT solely for the investigation of its effects on the bacterial profile of patients with rUTI has indicated that uropathogen abundance in these patients’ gut microbiomes is low and that gene carriage in those pathogens found to carry antibiotic resistance persisted at similar levels after FMT 24 . These contradictory findings suggest a persisting lack of clarity regarding FMT’s effects on the urinary microbiome of patients with rUTI.…”