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This study investigated recent trends in antibiotic use and factors associated with antibiotic use among children with acute infectious diarrhea. We obtained records of outpatients aged under 18 years diagnosed with acute infectious diarrhea from the Japan Medical Data Center database during 2012–2015.We investigated prescription patterns of antibiotics at their initial visit and evaluated factors associated with antibiotic usage using multivariable log-binomial regression models.Overall, we identified 4493 patients diagnosed with acute infectious diarrhea; 29.6% received antibiotics. The most commonly prescribed antibiotic is fosfomycin (20.3%). In multivariable log-binomial regression analysis, out-of-hour visits, clinical diagnoses of suspected bacterial enterocolitis, private outpatient clinics, and pediatric departments are significantly associated with higher prevalence of antibiotic use.Antibiotics are over-prescribed for children with acute infectious diarrhea. Our investigation provides important information to promote education of physicians and of health policy considerations for appropriate antibiotic prescription practices.