Gut Microbiota structure and ESBL-Enterobacteriaceae colonization in hospitalized versus healthy children

Abstract

Background: The intestinal microbiota plays a critical role in host health, particularly during early life when microbial colonization and immune development are still evolving. Disruption of this ecosystem (dysbiosis) has been increasingly linked to gastrointestinal disease and the emergence of antimicrobial-resistant organisms. Among these, extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-EB) are of particular concern due to their capacity for persistent gut colonization and transmission. Methods: This study investigated the intestinal microbiota composition of young children (≤3 years) with acute gastroenteritis compared with healthy controls. Fecal samples were analyzed using 16S rRNA gene–based approaches to characterize key bacterial taxa and assess differences in microbial diversity, structure, and abundance between groups. Results: Hospitalized children exhibited marked alterations in gut microbiota composition, including depletion of beneficial commensal taxa such as Faecalibacterium and members of the phylum Bacillota, alongside changes in Bacteroides-associated populations. Opportunistic and potentially pathogenic bacteria, particularly within the Enterobacteriaceae family, were consistently enriched. In contrast, probiotic-associated genera, including Bifidobacterium and Lactobacillus, showed variable patterns across samples without a consistent directional change, suggesting inter-individual variability in their abundance. ESBL colonization was associated with compositional differences in the microbial community, characterized by shifts toward facultative anaerobes and reduced representation of taxa associated with colonization resistance. Conclusion: These findings indicate that indicate that alterations in the gut microbiota in early childhood is closely associated with susceptibility to both gastrointestinal disease and colonization by antimicrobial-resistant organisms. Changes of key butyrate-producing and barrier-supporting taxa may facilitate the persistence of ESBL-producing Enterobacteriaceae. This study provides insights into the compositional and ecological differences of the pediatric gut microbiome during hospitalization and highlights the potential relevance of microbiota-targeted approaches, including dietary modulation and probiotic interventions, in the context of antimicrobial resistance.