Exploring recurrent urinary tract infection: paired microbiota and culture-based profiling reveals stable dysbiosis and multidrug-resistant, virulence-enriched uropathogens
- 1Department of Food Science and Technology, Pondicherry University
Abstract
**Objectives:** Recurrent urinary tract infection (rUTI) is increasingly complicated by antimicrobial resistance (AMR), yet urinary microbiome dysbiosis and isolate-level resistance-virulence are rarely examined together across different treatment states. In this study, we characterized both within the same sample in rUTI and in healthy controls. **Methods:** In this cross-sectional cohort, mid-stream urine was collected from women with untreated, treated and prophylaxis rUTI and age-matched healthy controls at four centres in South India. Of 80 samples collected, 75 were analysed (26 controls, 20 untreated, 20 treated, 9 prophylaxis) by 16S rRNA V3-V4 sequencing. In addition, 105 culturable isolates from the same samples were identified and tested for antimicrobial susceptibility (VITEK 2) and phenotypic virulence. **Results:** rUTI groups showed approximately half the alpha diversity of controls (median Shannon 1.07-1.18 vs 2.17; Kruskal-Wallis p = 0.041). Community structure differed from controls in every rUTI subgroup (PERMANOVA R-squared = 0.091, p = 0.004; pairwise FDR = 0.008) but not among subgroups. Mean Lactobacillus relative abundance fell from 29.2% in controls to <=13.2% in rUTI groups, while Escherichia-Shigella rose from 7.2% to 25.0-43.0%. Control-referenced dysbiosis z-scores were elevated in all rUTI groups (community distance: FDR <= 0.003; uropathogen: Lactobacillus index: FDR < 0.001 for treated and prophylaxis groups). Among isolates, Escherichia coli predominated (35/105; 16/35, 45.7% multidrug-resistant), followed by Klebsiella spp. (32% multidrug-resistant); carbapenem susceptibility was largely retained, and multidrug-resistant E. coli co-carried more virulence traits. **Conclusions:** rUTI is associated with a stable dysbiotic state that treatment does not restore, combining Lactobacillus loss and uropathogen dominance with a multidrug-resistant culturable reservoir that co-accumulates virulence traits. Reading the community and its isolates together may support microbiome-sparing, resistance-aware management of rUTI.
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BibTeX
@misc{kaushik2026exploring,
title = {{Exploring recurrent urinary tract infection: paired microbiota and culture-based profiling reveals stable dysbiosis and multidrug-resistant, virulence-enriched uropathogens}},
author = {S. Kaushik and K. P and S. Pal and N. Nandi and G. S. Kiran and S. H. K. Kumar and J. Selvin and V. N. Veettil and S. Devi},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.10.758225},
url = {https://www.biorxiv.org/content/10.64898/2026.10.10.758225v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Exploring recurrent urinary tract infection: paired microbiota and culture-based profiling reveals stable dysbiosis and multidrug-resistant, virulence-enriched uropathogens
AU - S. Kaushik
AU - K. P
AU - S. Pal
AU - N. Nandi
AU - G. S. Kiran
AU - S. H. K. Kumar
AU - J. Selvin
AU - V. N. Veettil
AU - S. Devi
PY - 2026
DA - 2026/10/10
PB - bioRxiv
DO - 10.64898/2026.10.10.758225
UR - https://www.biorxiv.org/content/10.64898/2026.10.10.758225v1
AB - **Objectives:** Recurrent urinary tract infection (rUTI) is increasingly complicated by antimicrobial resistance (AMR), yet urinary microbiome dysbiosis and isolate-level resistance-virulence are rarely examined together across different treatment states. In this study, we characterized both within the same sample in rUTI and in healthy controls. **Methods:** In this cross-sectional cohort, mid-stream urine was collected from women with untreated, treated and prophylaxis rUTI and age-matched healthy controls at four centres in South India. Of 80 samples collected, 75 were analysed (26 controls, 20 untreated, 20 treated, 9 prophylaxis) by 16S rRNA V3-V4 sequencing. In addition, 105 culturable isolates from the same samples were identified and tested for antimicrobial susceptibility (VITEK 2) and phenotypic virulence. **Results:** rUTI groups showed approximately half the alpha diversity of controls (median Shannon 1.07-1.18 vs 2.17; Kruskal-Wallis p = 0.041). Community structure differed from controls in every rUTI subgroup (PERMANOVA R-squared = 0.091, p = 0.004; pairwise FDR = 0.008) but not among subgroups. Mean Lactobacillus relative abundance fell from 29.2% in controls to <=13.2% in rUTI groups, while Escherichia-Shigella rose from 7.2% to 25.0-43.0%. Control-referenced dysbiosis z-scores were elevated in all rUTI groups (community distance: FDR <= 0.003; uropathogen: Lactobacillus index: FDR < 0.001 for treated and prophylaxis groups). Among isolates, Escherichia coli predominated (35/105; 16/35, 45.7% multidrug-resistant), followed by Klebsiella spp. (32% multidrug-resistant); carbapenem susceptibility was largely retained, and multidrug-resistant E. coli co-carried more virulence traits. **Conclusions:** rUTI is associated with a stable dysbiotic state that treatment does not restore, combining Lactobacillus loss and uropathogen dominance with a multidrug-resistant culturable reservoir that co-accumulates virulence traits. Reading the community and its isolates together may support microbiome-sparing, resistance-aware management of rUTI.
ER -