Sources and transmission dynamics of Campylobacter and Shigella using culture-independent molecular methods in Tanzania (SCAT): a protocol for a prospective observational cohort study

Introduction: Enteric infections caused by Shigella and Campylobacter species are associated with acute diarrhea as well as enteric dysfunction leading to chronic malnutrition and poor child development. However, interventional studies to reduce exposure to these pathogens have been ineffective, and evidence that identifies putative sources and species transmission dynamics between humans, animals and the environment is scarce. Because isolation of these organisms from both human and environmental samples is challenging, studies using molecular detection may help reduce this substantial knowledge gap and lead to targeted interventions to reduce the burden of disease. Methods and analysis: This longitudinal cohort study will enroll 100 index infants as well as their families in Haydom, Tanzania. Families will be followed for one year, with collection of stool samples monthly and during incident diarrhea from all household members. Additionally, we will sample from the index child's environment, including domestic animal stools, drinking water, milk, porridge, flies, and soil. All samples will undergo nucleic acid extraction and quantitative PCR for Campylobacter and Shigella. Serial serologic tests will also be performed to identify seroconversion to these pathogens. Associations between pathogen detection from the environment and household members and detection in index children will be estimated, and the temporal patterning of infection cases will be analyzed using transmission models. Ethics and dissemination: This trial has been approved by the Tanzanian National Institute for Medical Research and the University of Virginia Institutional Review Board.