LMIC human infant stool whole-genome shotgun metagenomic sequencing

Campylobacter sp. are a major cause of bacterial diarrhea worldwide and are associated with high rates of mortality and linear growth faltering in children living in low- to middle-income countries (LMICs). Campylobacter jejuni and C. coli are most often the causative agents of enteric disease among children in LMICs. However, there are many stool samples from children under 2 years of age with acute diarrheal disease or asymptomatic carriers living in a low resource community in Peru that are qPCR positive for Campylobacter species but qPCR negative for C. jejuni and C. coli. The goal of this study was to determine if whole-genome shotgun metagenomic sequencing (WSMS) could identify the Campylobacter species within these samples.