Environmental Exposures Associated with Enteropathogen Infection in Six-Month-Old Children Enrolled in the ECoMiD Cohort along a Rural–Urban Gradient in Northern Ecuador

Enteropathogens are major contributors to mortality and morbidity, particularly in settings with limited access to water, sanitation, and hygiene infrastructure. To assess transmission pathways associated with enteropathogen infection, we measured household environmental conditions and assayed 22 enteropathogens using TaqMan Array Cards in stool samples from 276 six-month-old children living in communities along a rural-urban gradient in Northern Ecuador. We utilized multivariable models, risk factor importance, and distance-based statistical methods to test factors associated with infection. Most children (89%) carried at least one pathogen, and 72% carried two or more. Bacterial infections (82% of participants) were more common than viruses (58%) or parasites (9.1%). Infants living in the urban site had decreased infection risks compared to those in rural locations. Improved water and sanitation were most predictive of reduced infection risk. Improved water was associated with decreased enterotoxigenic <i>E. coli</i> prevalence, and improved sanitation was associated with lower prevalence of any infection and specifically norovirus. Animal exposure was associated with increased <i>Salmonella</i> prevalence. Children measured during the rainy season had fewer viral and more bacterial infections. Identifying environmental exposures associated with specific pathogen outcomes provides insights into transmission pathways, which contribute critical information for developing effective strategies to improve child health.