Microbiome Disruption Caused by Antibiotic Overuse in Pediatric Gastroenteritis: A Systematic Review Publisher



Jafari M ; Malekian Taghi A ; Shabanimirzaee H ; Ashraf Talesh S ; Shafiei A ; Eftekhari K
Source: Archives of Pediatric Infectious Diseases Published:2026

Abstract

Context: This systematic review examines pediatric gastroenteritis, a prevalent global condition, most commonly of viral origin, with rotavirus, norovirus, and adenovirus as the leading pathogens. Despite this, antibiotics are frequently and inappropriately prescribed, especially in cases without confirmed bacterial etiology, contributing to unnecessary harm. Objectives: This systematic review evaluates the adverse consequences of antibiotic overuse in pediatric gastroenteritis, with emphasis on microbial resistance, gut microbiome disruption, and the risk of severe complications such as Clostridioides difficile infection and hemolytic uremic syndrome (HUS). Data Sources: A systematic search was conducted across PubMed, Embase, Scopus, and Cochrane Library for studies published between 2005 and 2025. Study Selection: Eligible studies included randomized controlled trials, cohort studies, and systematic reviews evaluating antibiotic-related outcomes in children (< 18 years) with clinically or laboratory-confirmed viral gastroenteritis. Data Extraction: The quality of the studies was evaluated using both the Cochrane risk-of-bias tool and the Newcastle-Ottawa Scale. Results: Forty studies met inclusion criteria. Inappropriate antibiotic use in viral gastroenteritis cases was associated with altered gut microbial diversity, increased colonization by opportunistic pathogens, and higher risk of secondary infections. Use of broad-spectrum antibiotics was especially associated with negative effects such as extended disease duration, the development of antimicrobial resistance (AMR), and a higher rate of C. difficile colitis. Using antibiotics to treat Shiga toxin-producing Escherichia coli gastroenteritis considerably raised the likelihood of HUS occurrence. Conclusions: Antibiotic overuse in viral pediatric gastroenteritis poses serious individual and public health risks. Clinical guidelines should emphasize accurate viral diagnosis, supportive care, and restraint in prescribing antibiotics. Strengthened antibiotic stewardship and increased awareness are essential to prevent long-term complications and preserve microbiome integrity in children. Copyright © 2026, Jafari et al.