Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa

Abstract

INTRODUCTION: Enteric bacterial pathogens are a major cause of diarrhoeal disease in low-income and middle-income countries, with complex transmission pathways involving human, animal and environmental reservoirs. Conventional epidemiological and microbiological approaches provide important insights into pathogen burden and distribution but lack the resolution needed to characterise fine-scale diversity, antimicrobial resistance (AMR) and transmission dynamics. Whole-genome sequencing offers high-resolution tools to investigate these processes within a One Health framework. METHODS AND ANALYSIS: in Africa (GETCampy-Africa) study uses a multicountry, One Health design to investigate pathogen diversity, source attribution and transmission pathways. The study uses a case-control framework, recruiting children with medically attended diarrhoea and asymptomatic community controls across sites in Burkina Faso, Ghana and The Gambia. Samples were collected from human participants, domestic animals and environmental sources following standardised protocols. Participant enrolment and sample collection have been completed, while laboratory processing, sequencing and genomic analyses are ongoing. Genomic data are analysed to assess population structure, AMR profiles and probabilistic attribution of isolates to potential reservoirs using comparative genomics and machine learning approaches. ETHICS AND DISSEMINATION: Ethical approval was obtained from relevant national and institutional committees in all participating countries. Written informed consent was obtained from participants or their guardians prior to enrolment. Findings will be disseminated through peer-reviewed publications, stakeholder engagement activities and open-access platforms to support public health interventions and policy development.