Chronic urinary tract infections (UTIs) are a debilitating condition characterised by persistent or recurrent bladder infections that often evade immune clearance and resist standard antibiotic treatment, leaving patients symptomatic for years. Diagnosis is challenging because uropathogenic bacteria can embed within the urothelium, escaping detection in conventional midstream urine cultures. To address this, we aimed to identify predictive multi-omic signatures of chronic UTI using a translational murine model.
Female C3H/HeNRj mice (6-8 weeks old) were inoculated with the clinical uropathogenic Escherichia coli strain UTI89 or sham-inoculated with sterile PBS. At 28 days post-infection (dpi), urinary bladder bacterial load was assessed to retrospectively stratify mice as having persistent (chronic) or resolved infections. Bulk RNA sequencing was also performed on bladder tissue collected at 28 dpi. Longitudinal urine and faecal samples were collected weekly from 7 days before infection to 28 dpi and analysed using untargeted metabolomics and shotgun metagenomic sequencing, respectively.
Mice with chronic infection exhibited markedly altered bladder transcriptomic profiles, with signatures of persistent immune activation and chronic inflammation. In contrast, transcriptomes from mice that had resolved the infection closely resembled those of sham-inoculated controls. The urinary metabolome of chronically infected mice was enriched over time with metabolites and lipids linked to immune dysregulation and cell membrane damage, while mice that had resolved the infection displayed increased levels of antioxidant-associated metabolites, suggesting a more effective immune response. Distinct faecal microbiome profiles were detectable as early as 7 dpi in mice that later developed chronic infection, with several bacterial species consistently differentially abundant across the time course.
Together, these findings reveal unique bladder transcriptomic, urinary metabolomic, and faecal microbiome signatures predictive of chronic UTI. This integrated multi-omic approach lays the foundation for early biomarker-driven diagnostics and novel therapeutic strategies to tackle treatment-refractory chronic UTIs.