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.

Keywords: IBCs; UPEC; UTI; adolescent; chronic; intracellular bacterial communities; pediatric; urinary tract infection; uropathogenic E. coli.

Fig 1

Case summary of a 14-year-old girl with chronic UTI and persistent IBCs. (A) Patient symptoms, treatment timeline, and corresponding findings from urine samples. Research samples were tested for intracellular E. coli using microscopy, with urinary cytokine quantification. Some of the IBC images are mini versions of images displayed in Fig. 2, in greater detail. (B) Cystoscopy, done November 2023, identified extensive keratinizing squamous metaplasia of the bladder mucosa. (C and D) Desquamated epithelial cells demonstrated extensive IBCs under spinning disk confocal microscopy (stained in blue with Wright stain), displaying different phenotypes. Created with BioRender.com. IBC, intracellular bacterial community; UTI, urinary tract infection.

Fig 2

Spinning disk confocal microscopy of urothelial cells with intracellular E. coli. Samples were stained with antibodies against E. coli (green), uroplakins (white), wheat germ agglutinin (pink), and 4′,6-diamidino-2-phenylindole for the cell nucleus (purple). Representative images of urothelial cells isolated from urine cultures in (A) November 2023 (sample 1), (B) January 2024 (sample 2, also shown in Fig. 1), and (C) April 2024 (sample 3). Scale bar denotes 50 μm. (D) Percentage of imaged exfoliated cells with IBCs across the three samples. One-sample Wilcoxon t-test was used to assess statistical significance as indicated. IBC, intracellular bacterial communities.

Fig 3

E. coli localization in desquamated epithelial cells. IBCs were imaged using SDCM with subsequent quantification. SDCM image depicting UPEC biofilm communities (green) in cells stained with UPIIIa (pink) (A). A representative MFI plot shows the location of the UPEC signal relative to the UPIIIa and DAPI signal along the longitudinal ROI along the y-axis, as well as a cross-section slice on the average taken from different representative images (B and C). No. of ROIs analyzed per sample = 40. Scalebar = 10 micrometres. DAPI, 4′,6-diamidino-2-phenylindole; IBC, intracellular bacterial community; MFI, mean fluorescence intensity; ROI, region of interest; SDCM, spinning disk confocal microscopy; UPIIIa, uroplakin 3a.

Fig 4

MICs determined for the UPEC strains isolated from each sample. Microdilution assays were performed on UPEC isolates from the three research samples according to EUCAST guidelines to determine the MICs of isolated E. coli strains to (A) cephalexin and (B) trimethoprim. (C) MIC₉₀ (concentration at which 90% of bacteria are killed) for both antibiotics. UTI1 and UTI2 were isolated from intracellular reservoirs in urothelial cells. UTI3 was isolated from extracellular urine culture. MIC, minimum inhibitory concentration.

Fig 5

Urinary cytokine profile in a 14-year-old girl with chronic UTI over a 6-month period. Enzyme-linked immunosorbent sandwich assays were done on freshly collected urine samples to quantify key urinary cytokines, with each sample performed in triplicate. Comparisons were drawn between levels of IL-6, IL-8, TNF-α, and IL-1β (A–D) in urine samples obtained 3 months apart. Dunnett’s T3 multiple comparison tests were used to assess statistical significance for relevant comparisons, as indicated.