Continuous Antibiotic Prophylaxis for Vesicoureteral Reflux: Impact on the Pediatric Microbiome—A Systematic Review

TL;DR

Long-term low-dose antibiotics in infants with a urinary tract condition change gut bacteria composition but keep overall diversity stable, suggesting a need for microbiome-aware treatment strategies.

Contribution

This systematic review identifies specific microbiome shifts and resistance changes from continuous antibiotic prophylaxis in infants with vesicoureteral reflux.

Findings

CAP preserves gut microbial diversity but increases Enterobacteriaceae and decreases Bifidobacteriaceae.

Core gut functions like short-chain fatty acid production remain stable despite antibiotic use.

Prolonged CAP may expand antimicrobial resistance and increase non–E. coli infections.

Abstract

What are the main findings?
Continuous antibiotic prophylaxis (CAP) in children with vesicoureteral reflux preserves overall gut microbial diversity but induces subtle compositional shifts, including enrichment of Enterobacteriaceae and reduction in Bifidobacteriaceae.Functional analyses show that the core fermentative capacity of the gut microbiota (e.g., short-chain fatty acid production) remains stable under CAP, although the resistome may expand with prolonged exposure.
What are the implications of the main findings?
Even mild antibiotic-driven dysbiosis during infancy may influence immune and metabolic development, underscoring the need for microbiome-aware prophylaxis strategies.Identifying microbiome alterations could guide personalized interventions—such as optimized antibiotic regimens, shorter prophylaxis duration, or probiotic supplementation—to preserve microbial health while preventing urinary tract infections.

Continuous antibiotic prophylaxis (CAP) in children with vesicoureteral reflux preserves overall gut microbial diversity but induces subtle compositional shifts, including enrichment of Enterobacteriaceae and reduction in Bifidobacteriaceae.

Functional analyses show that the core fermentative capacity of the gut microbiota (e.g., short-chain fatty acid production) remains stable under CAP, although the resistome may expand with prolonged exposure.

Even mild antibiotic-driven dysbiosis during infancy may influence immune and metabolic development, underscoring the need for microbiome-aware prophylaxis strategies.

Identifying microbiome alterations could guide personalized interventions—such as optimized antibiotic regimens, shorter prophylaxis duration, or probiotic supplementation—to preserve microbial health while preventing urinary tract infections.

Background: Continuous antibiotic prophylaxis (CAP) is widely used in infants with vesicoureteral reflux (VUR) to prevent recurrent urinary tract infections and renal scarring. However, this practice entails prolonged low-dose antibiotic exposure during a critical period of microbiome establishment, potentially influencing long-term microbial and immune development. Methods: A systematic review was conducted according to PRISMA 2020 guidelines. PubMed, Embase, Scopus, Web of Science, and the Cochrane Library were searched up to September 2025 for studies evaluating gut or urinary microbiome changes in children receiving CAP for VUR. Eligible studies included human participants under 18 years with microbiome outcomes assessed by sequencing or culture-based methods. Results: Twenty-one records were identified, and four studies met inclusion criteria—three observational microbiome studies and one randomized controlled trial. CAP preserved overall microbial alpha diversity but induced compositional changes, notably enrichment of Enterobacteriaceae and reduction in Bifidobacteriaceae. The included RCT confirmed reduced UTI recurrence but increased antimicrobial resistance and non–E. coli infections. Conclusions: CAP in early life maintains microbial diversity but alters microbiota composition and resistance profiles. Identifying these shifts may support individualized prophylaxis strategies and microbiome-preserving interventions to balance infection prevention with ecological safety in infancy.

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