{
  "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 The Genomic Epidemiology and Transmission of Campylobacter 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.",
  "authors": [
    {
      "affiliations": [
        "Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK",
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Henry Badji"
    },
    {
      "affiliations": [
        "Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand",
        "Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK",
        "Department of Biology, University of Oxford, Oxford, UK"
      ],
      "name": "Ben Pascoe"
    },
    {
      "affiliations": [
        "Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK",
        "Department of Biology, University of Oxford, Oxford, UK"
      ],
      "name": "Madison P Goforth"
    },
    {
      "affiliations": [
        "Zoonosis Science Center, Uppsala University, Uppsala, Sweden"
      ],
      "name": "Evangelos Mourkas"
    },
    {
      "affiliations": [
        "Laboratory of Molecular Biology, Epidemiology and Monitoring of Bacteria and Virus Transmitted by Food (LaBESTA), Universite Joseph Ki-Zerbo, Ouagadougou, Burkina Faso"
      ],
      "name": "Evariste Bako"
    },
    {
      "affiliations": [
        "Laboratory of Molecular Biology, Epidemiology and Monitoring of Bacteria and Virus Transmitted by Food (LaBESTA), Universite Joseph Ki-Zerbo, Ouagadougou, Burkina Faso"
      ],
      "name": "Isidore JO Bonkoungou"
    },
    {
      "affiliations": [
        "Laboratory of Molecular Biology, Epidemiology and Monitoring of Bacteria and Virus Transmitted by Food (LaBESTA), Universite Joseph Ki-Zerbo, Ouagadougou, Burkina Faso"
      ],
      "name": "Modeste T Gampene"
    },
    {
      "affiliations": [
        "Laboratory of Molecular Biology, Epidemiology and Monitoring of Bacteria and Virus Transmitted by Food (LaBESTA), Universite Joseph Ki-Zerbo, Ouagadougou, Burkina Faso"
      ],
      "name": "Marguerite Edith Malatala Nikiema"
    },
    {
      "affiliations": [
        "Laboratory of Molecular Biology, Epidemiology and Monitoring of Bacteria and Virus Transmitted by Food (LaBESTA), Universite Joseph Ki-Zerbo, Ouagadougou, Burkina Faso"
      ],
      "name": "Barthélemy S Zoma"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Ousman E Bah"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Eustacia Jane Cassell"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Abdoulie K Ceesay"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Bubacarr E Ceesay"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Ousman Ceesay"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Bakary Conteh"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Lamin Drammeh"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Binta Faye"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Abdoulie F Jallow"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Fatima Jallow"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Ousman Jallow"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Samba Juma Jallow"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Pa Modou Joof"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Modou Kandeh"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Mehrab Karim"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Jarra Manneh"
    },
    {
      "affiliations": [
        "Department of Livestock Services, Government of the Gambia, Abuko, Gambia"
      ],
      "name": "Abdou Ceesay"
    },
    {
      "affiliations": [
        "Department of Livestock Services, Government of the Gambia, Abuko, Gambia"
      ],
      "name": "Ebrima Fofana"
    },
    {
      "affiliations": [
        "Department of Livestock Services, Government of the Gambia, Abuko, Gambia"
      ],
      "name": "Mamud Jallow"
    },
    {
      "affiliations": [
        "Department of Livestock Services, Government of the Gambia, Abuko, Gambia"
      ],
      "name": "Modou B Jarju"
    },
    {
      "affiliations": [
        "Ministry of Health, Regional Health Directorate, Government of the Gambia, Banjul, Gambia"
      ],
      "name": "Samba Bah"
    },
    {
      "affiliations": [
        "Ministry of Health, Regional Health Directorate, Government of the Gambia, Banjul, Gambia"
      ],
      "name": "Dodou Sanyang"
    },
    {
      "affiliations": [
        "National Agricultural Research Institute, Banjul, Gambia"
      ],
      "name": "Demba B Jallow"
    },
    {
      "affiliations": [
        "Department of Clinical Microbiology, University for Development Studies, Tamale, Ghana"
      ],
      "name": "Mukaila I Alebiosu"
    },
    {
      "affiliations": [
        "Faculty of Biosciences, University for Development Studies, Tamale, Ghana"
      ],
      "name": "Atanyiwoen Brusah"
    },
    {
      "affiliations": [
        "Department of Clinical Microbiology, University for Development Studies, Tamale, Ghana"
      ],
      "name": "Akosua Bonsu Karikari"
    },
    {
      "affiliations": [
        "Faculty of Biosciences, University for Development Studies, Tamale, Ghana"
      ],
      "name": "Courage KS Saba"
    },
    {
      "affiliations": [
        "Department of Microbiology, University of Helsinki, Helsinki, Finland"
      ],
      "name": "Kaisa Haukka"
    },
    {
      "affiliations": [
        "Centre for Environmental Policy, Imperial College London, London, UK"
      ],
      "name": "C Matilda (Tilly) Collins"
    },
    {
      "affiliations": [
        "Centre for Environmental Policy, Imperial College London, London, UK"
      ],
      "name": "Adrian W Leach"
    },
    {
      "affiliations": [
        "Centre for Environmental Policy, Imperial College London, London, UK"
      ],
      "name": "Polina Levontin"
    },
    {
      "affiliations": [
        "Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK",
        "Department of Biology, University of Oxford, Oxford, UK",
        "Department of Life Sciences, University of Bath, Bath, UK"
      ],
      "name": "Shani UP Ali"
    },
    {
      "affiliations": [
        "Department of Biology, University of Oxford, Oxford, UK"
      ],
      "name": "Frances M Colles"
    },
    {
      "affiliations": [
        "Medical Microbiology and Infectious Diseases, Swansea University Medical School, Swansea, UK"
      ],
      "name": "Matthew David Hitchings"
    },
    {
      "affiliations": [
        "Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK",
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Martin Antonio"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "Abdul Karim Sesay"
    },
    {
      "affiliations": [
        "Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK"
      ],
      "name": "Ozan Gundogdu"
    },
    {
      "affiliations": [
        "Medical Research Council (UK) (MRC) Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia"
      ],
      "name": "M Jahangir Hossain"
    },
    {
      "affiliations": [
        "Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK",
        "Department of Biology, University of Oxford, Oxford, UK"
      ],
      "name": "Samuel K Sheppard"
    }
  ],
  "title": "Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa",
  "uid": "c4953a42-d570-57de-89dc-e90256f07f88"
}