Molecular Detection of Pathogens Associated with Childhood Gastroenteritis in Burkina Faso Using the FilmArray® GI Panel

Background Acute gastroenteritis (AGE) is a major cause of morbidity and mortality in children under five years of age in low- and middle-income countries. AGE in children is associated with a wide range of bacterial, viral, and parasitic pathogens. The aim of this study was to investigate the epidemiology of infectious agents responsible for AGE in hospitalized children under five years of age at Bogodogo University Hospital. Methods A prospective, descriptive study was conducted from December 2017 to November 2018. A total of 90 stool samples were collected from hospitalized children under 5 years of age presenting with AGE. Samples were analyzed for the presence of 22 pathogens using the FilmArray® gastrointestinal panel. Results At least one pathogen was detected in 74.4% (67/90) of patients. Mono-infections accounted for 44.7% (30/67) of positive cases, while co-infections accounted for 55.2% (37/67). Viruses and bacteria were the most common types of pathogens, each detected in 58.8% (53/90) of cases, followed by parasites in 30% (27/90). The most frequently detected bacterial pathogen was diarrheagenic Escherichia coli (DEC) (48.8%). Rotavirus (22.2%) and Giardia lamblia (16.6%) were also prevalent. Viral infections predominated in children under 12 months (55.1%), whereas bacterial infections were more frequent in children aged 13–24 months (82.1%). Fever was the most common associated symptom, reported in 76.1% of cases Conclusion This study highlights bacteria, particularly DEC, as the most prevalent pathogens responsible for infectious diarrhea in children under five in Burkina Faso. The FilmArray® GI panel proved valuable for rapid, comprehensive pathogen detection, supporting improved diagnosis and management of childhood diarrhea.