ENTERIC VIRAL DETECTION AND BACTERIAL MICROBIOME PROFILES IN CHILDREN UNDER FIVE YEARS WITH ACUTE GASTROENTERITIS IN EMBU COUNTY, KENYA
This study aims to determine the prevalence and co-infection patterns of six enteric viruses, adenovirus, rotavirus, norovirus GI and GII, sapovirus, and astrovirus, among children aged five years and below presenting with acute diarrhoea at Embu Level V Hospital, Kenya. In a subset of five participants, metagenomic sequencing was used to describe the bacterial microbiome, including bacterial alpha diversity and relative taxonomic abundance. Sociodemographic, perinatal, nutritional, and clinical information was also examined to provide context for the observed pathogen and microbiome profiles.The study addresses the limited availability of multi-pathogen data from rural Kenyan settings. By examining viral detection, viral co-infections and bacterial microbiome characteristics together, it provides a broader description of acute diarrhoeal disease than single-pathogen testing alone. The findings may support local enteric disease surveillance and help identify priorities for future research, including larger studies of bacterial, viral and parasitic pathogens, adenovirus genotyping, rotavirus strain analysis, and the relationship between microbiome composition and clinical outcomes. Because the study is preliminary and the microbiome analysis includes only five participants, its findings should be considered exploratory rather than representative of all children in Embu County.