Background: Diarrheal infections are one of the leading causes of sickness and death all over the world. It is the second-most common cause of under-five mortality, accounting for over half a million deaths annually. In Abeokuta, the etiology of diarrheagenic bacteria and diarrheagenic viruses has not been well studied. Objective: To determine the prevalence of Enteropathogenic Escherichia coli and Rotavirus Antigen among Diarrheic Children attending Selected Hospitals in Abeokuta, Nigeria: A Comparative study. Methods: A total of 315 stool samples were collected from children 0–5 years of age across three selected hospitals. With a wooden spatula, 5ml of fecal sample was scooped and decanted into clean, labeled screw-capped tubes. Rotavirus antigen screening was performed according to the manufacturers’ instructions, while EPEC screening was performed using cultural, biochemical, and stereotyping methods. Results: From the sample screening performed, 30 (37.04%) were EPEC positive, whereas 51 (62.96%) were positive for rotavirus. Dissemination of children based on ageshowed that children between 7–12 months had the most elevated predominance of Rotavirus infection 17 (33.33%) while the lowest predominance was observed in children between 0–2 months 4 (7.84%). Furthermore, the highest predominance of EPEC diseases was observed in children between 7–12 months 12 (40%) and the lowest predominance in children between 19–24 months 2 (6.67%). Conclusion: This study had demonstrated a higher prevalence of Rotavirus infection as compared to EPEC diseases among Diarrheic Children within the study location.
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