Severe chronic UTI sustained by clinically undetected intracellular Escherichia coli in a pediatric patient

ABSTRACT

Background

The presence of intracellular bacterial communities (IBCs) in the urothelium has been well documented in adults with chronic urinary tract infections (UTIs), but its long-term persistence going undetected in a severely symptomatic adolescent has not been reported.

Case Summary

We present the case of a 14-year-old girl suffering from debilitating chronic UTI symptoms and associated urinary incontinence for many years. Multiple antibiotic courses provided only temporary relief, with positive Escherichia coli cultures recurring promptly after each treatment cycle. A recently conducted cystoscopy (after >6 years of persistent symptoms) revealed widespread squamous metaplasia of the bladder wall, and enhanced urinary analysis identified extensive intracellular bacterial (E. coli) communities in exfoliated urothelial cells. These intracellular bacterial communities persisted even when the urine became transiently culture negative on antibiotic treatment. Evidence from confocal microscopy demonstrated extensive intracellular E. coli, which may serve as a bacterial reservoir that seeds urinary reinfection when antibiotics are ceased. Persistent intracellular bacteria were not detected by routine urine microscopy and culture. Analysis of urinary cytokines suggested chronic inflammation of the bladder wall, driven by persistent bacterial infection, as the potential cause for the unrelenting symptoms.

Conclusion

This is the first report demonstrating long-term undetected IBC in a severely symptomatic child with chronic UTI. It underscores the need to learn more about intracellular bacteria and urinary tract biofilms that are protected from antibiotics and host immunity. IBC reservoirs seem to drive bladder wall inflammation, exacerbating clinical symptoms and increasing the risk of long-term adverse sequelae.

Manoharan A, Wijekoon N, Whiteley G, Ashishkumar TD, Flores-Rodriguez N, Jensen SO, Söderström B, Moore KH, Manos J, Marais BJ, Deshpande A.2026.Severe chronic UTI sustained by clinically undetected intracellular Escherichia coli in a pediatric patient. ASM Case Rep2:e00077-25.https://doi.org/10.1128/asmcr.00077-25