Zoonotic and Environmental Sources of Infant Enteric Pathogen Infections Identified with Longitudinal Sampling

Many enteric pathogens that infect young children can be zoonotic, yet the exposure risk of domestic animals living in close proximity to young children is poorly understood. Here, we longitudinally measured 33 enteric pathogens in child stool, animal feces, and the household environment (n = 28,743 pathogen-sample observations) to investigate pathogen transmission between animals and children under two in pastoralist communities in rural Northern Kenya. Children were typically infected with 1 enteric pathogen by 3 months of age, and pathogen burden increased with age; 85% of enteric pathogens detected in child stool were also detected in animal feces. New infections in children were associated with preceding household detection of the same pathogen in soil (Odds ratio: 8.8, 95% confidence interval: 3.3-23) and on child hands (odds ratio: 5.0, 95% confidence interval 1.1-17). Regression modeling revealed transmission of pathogens from poultry, dog, and ruminant feces to household soil, and between child hands and child stool. Our results provide new evidence that domestic animals in the household environment contribute to early life enteric pathogen exposure, and that child hand hygiene could substantially prevent animal-child transmission.