Application of next generation sequencing for detection of multiple pathogens in children with acute diarrhea

Abstract

Diarrhea cause high mobidity and mortality in children under 5 years of age, especially for developing countries like Viet Nam. Apart from rotavirus, known to be the most important cause of acute diarrhea in chidren, more than 20 pathogens have been identifed. However, there is still 20% of diarrheal cases with unknown cause worldwide. This study aimed to apply of next generation sequencing for detection of multiple pathogens in children with acute diarrhea. Fecal samples from rotavirus vaccinated chidren were collected and tested for common pathogens by realtime RT-PCR and ELISA. For NGS 3-4 samples were pooled and analysed. Twenty-fve and ffteen groups of pathogens were identifed in fecal samples from Vietnamese and Belgium children. Apart from the members of the Picornavirdae, Caliciviridae family, uncommon members from Parvoviridae,
bacteriophage of V. cholera, Samonella were identifed in Vietnam. Thus, NGS could serve as an useful tool to identify multiple pathogens including new pathogens in Vietnam.