Urinary Microbiome Dysbiosis in Children With Congenital Uropathies at Varying Risk for Urinary Tract Infections

Background Febrile urinary tract infections (UTIs) may occur in 30–50% of children with vesicoureteral reflux (VUR) or posterior urethral valves (PUV), frequently leading to renal scarring despite chemoprophylaxis. Around 15 % of children with uretero-pelvic junction obstruction (UPJO) may also develop UTIs. Yet investigations that can identify at-risk children before the first episode of UTI are lacking. In this exploratory study, we investigated the pre-infection urinary microbiome in Indian children with congenital anomalies of the kidney and urinary tract (CAKUT) to determine whether microbiome alterations, metabolic potential and antibiotic resistance profiles precede UTI. Materials and Methods In this prospective cohort study with follow-up, urine samples were collected from 80 children: 36 with newly diagnosed, antibiotic-naïve CAKUT patients (18 UPJO, 12 VUR, 6 PUV) and 44 controls. Patients were stratified a priori into low (n = 19) and high-risk (n = 17) groups using clinically defined UTI-susceptibility criteria. V3–V4 16S ribosomal ribonucleic acid sequencing defined urinary microbial profiles. Alpha- and beta-diversity were compared using Shannon index and permutational multivariate analysis of variance (PERMANOVA) respectively. Sliding-window and network-based analyses mapped dysbiosis gradients. Patients were followed longitudinally to assess UTI incidence. Identified dysbiosis-linked microbial markers at baseline were investigated using Kaplan-Meier and Cox-proportional hazard-based analyses as predictors of UTI-risk. Metabolic functions were inferred from taxonomic data. Antibiotic resistance patterns were characterized using CARD-RGI (Comprehensive Antibiotic Resistance Database – Resistance Gene Identifier) and WHO-AWaRe (World Health Organization Access, Watch, and Reserve) classification. Results Urinary microbial α-diversity declined significantly from controls to low-risk to high-risk groups (P = 0.002), accompanied by an increase in intra-group variability (P ≤ 0.005). PERMANOVA revealed distinct clustering by risk (R 2 = 0.11; P=0.001). Dysbiosis scores inversely correlated with the first Kendall PCoA axis (ρ = –0.62; P < 0.001). With increasing risk of UTI, the commensal, control-associated genera declined along this axis while the facultative pathogens became dominant. Control-associated microbiomes favoured short- and branched-chain fatty-acid and spermidine production; high-risk microbiomes over-produced ammonia, putrescine, and cadaverine. Resistance to 18/22 routinely tested antibiotics was almost confined to the 31 risk-associated microbiomes (P = 0.001). During the median (IQR) follow-up of 564 (518-594) months, 14 of 36 CAKUT children developed UTIs, and baseline depletion of health-associated microbial consortia correlated with reduced UTI-free survival. A panel of 10 species-level and 12 genus-level were identified as health-associated markers negatively associated with future UTI-risk during follow-up investigation. Conclusions Children with CAKUT exhibit urinary microbiome dysbiosis before their first symptomatic UTI, characterized by loss of conserved health-associated taxa, metabolic imbalance, and broad-spectrum antibiotic resistance. These findings support the potential of microbiome-informed, non-invasive risk stratification and microbiome-tailored prophylaxis, while establishing the first Indian paediatric reference set for CAKUT-related UTI prevention.