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

Henry Badji, Ben Pascoe Orcid Logo, Madison P Goforth, Evangelos Mourkas, Evariste Bako, Isidore JO Bonkoungou, Modeste T Gampene, Marguerite Edith Malatala Nikiema, Barthélemy S Zoma, Ousman E Bah, Eustacia Jane Cassell, Abdoulie K Ceesay, Bubacarr E Ceesay, Ousman Ceesay, Bakary Conteh, Lamin Drammeh, Binta Faye, Abdoulie F Jallow, Fatima Jallow, Ousman Jallow, Samba Juma Jallow, Pa Modou Joof, Modou Kandeh, Mehrab Karim, Jarra Manneh, Abdou Ceesay, Ebrima Fofana, Mamud Jallow, Modou B Jarju, Samba Bah, Dodou Sanyang, Demba B Jallow, Mukaila I Alebiosu, Atanyiwoen Brusah, Akosua Bonsu Karikari, Courage KS Saba, Kaisa Haukka, C Matilda (Tilly) Collins, Adrian W Leach, Polina Levontin, Shani UP Ali, Frances M Colles, Matthew Hitchings Orcid Logo, Martin Antonio, Abdul Karim Sesay, Ozan Gundogdu, M Jahangir Hossain Orcid Logo, Samuel K Sheppard

BMJ Open, Volume: 16, Issue: 6, Start page: e109566

Swansea University Author: Matthew Hitchings Orcid Logo

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DOI (Published version): 10.1136/bmjopen-2025-109566

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...

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ISSN: 2044-6055
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URI: https://cronfa.swan.ac.uk/Record/cronfa72176
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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&#x2013;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. 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Biomedical Science</level></path><authors><author><firstname>Henry</firstname><surname>Badji</surname><order>1</order></author><author><firstname>Ben</firstname><surname>Pascoe</surname><orcid>0000-0001-6376-5121</orcid><order>2</order></author><author><firstname>Madison P</firstname><surname>Goforth</surname><order>3</order></author><author><firstname>Evangelos</firstname><surname>Mourkas</surname><order>4</order></author><author><firstname>Evariste</firstname><surname>Bako</surname><order>5</order></author><author><firstname>Isidore JO</firstname><surname>Bonkoungou</surname><order>6</order></author><author><firstname>Modeste T</firstname><surname>Gampene</surname><order>7</order></author><author><firstname>Marguerite Edith Malatala</firstname><surname>Nikiema</surname><order>8</order></author><author><firstname>Barth&#xE9;lemy S</firstname><surname>Zoma</surname><order>9</order></author><author><firstname>Ousman E</firstname><surname>Bah</surname><order>10</order></author><author><firstname>Eustacia Jane</firstname><surname>Cassell</surname><order>11</order></author><author><firstname>Abdoulie K</firstname><surname>Ceesay</surname><order>12</order></author><author><firstname>Bubacarr E</firstname><surname>Ceesay</surname><order>13</order></author><author><firstname>Ousman</firstname><surname>Ceesay</surname><order>14</order></author><author><firstname>Bakary</firstname><surname>Conteh</surname><order>15</order></author><author><firstname>Lamin</firstname><surname>Drammeh</surname><order>16</order></author><author><firstname>Binta</firstname><surname>Faye</surname><order>17</order></author><author><firstname>Abdoulie F</firstname><surname>Jallow</surname><order>18</order></author><author><firstname>Fatima</firstname><surname>Jallow</surname><order>19</order></author><author><firstname>Ousman</firstname><surname>Jallow</surname><order>20</order></author><author><firstname>Samba Juma</firstname><surname>Jallow</surname><order>21</order></author><author><firstname>Pa Modou</firstname><surname>Joof</surname><order>22</order></author><author><firstname>Modou</firstname><surname>Kandeh</surname><order>23</order></author><author><firstname>Mehrab</firstname><surname>Karim</surname><order>24</order></author><author><firstname>Jarra</firstname><surname>Manneh</surname><order>25</order></author><author><firstname>Abdou</firstname><surname>Ceesay</surname><order>26</order></author><author><firstname>Ebrima</firstname><surname>Fofana</surname><order>27</order></author><author><firstname>Mamud</firstname><surname>Jallow</surname><order>28</order></author><author><firstname>Modou B</firstname><surname>Jarju</surname><order>29</order></author><author><firstname>Samba</firstname><surname>Bah</surname><order>30</order></author><author><firstname>Dodou</firstname><surname>Sanyang</surname><order>31</order></author><author><firstname>Demba B</firstname><surname>Jallow</surname><order>32</order></author><author><firstname>Mukaila I</firstname><surname>Alebiosu</surname><order>33</order></author><author><firstname>Atanyiwoen</firstname><surname>Brusah</surname><order>34</order></author><author><firstname>Akosua Bonsu</firstname><surname>Karikari</surname><order>35</order></author><author><firstname>Courage KS</firstname><surname>Saba</surname><order>36</order></author><author><firstname>Kaisa</firstname><surname>Haukka</surname><order>37</order></author><author><firstname>C Matilda (Tilly)</firstname><surname>Collins</surname><order>38</order></author><author><firstname>Adrian W</firstname><surname>Leach</surname><order>39</order></author><author><firstname>Polina</firstname><surname>Levontin</surname><order>40</order></author><author><firstname>Shani UP</firstname><surname>Ali</surname><order>41</order></author><author><firstname>Frances M</firstname><surname>Colles</surname><order>42</order></author><author><firstname>Matthew</firstname><surname>Hitchings</surname><orcid>0000-0002-5527-4709</orcid><order>43</order></author><author><firstname>Martin</firstname><surname>Antonio</surname><order>44</order></author><author><firstname>Abdul Karim</firstname><surname>Sesay</surname><order>45</order></author><author><firstname>Ozan</firstname><surname>Gundogdu</surname><order>46</order></author><author><firstname>M Jahangir</firstname><surname>Hossain</surname><orcid>0000-0002-8415-3180</orcid><order>47</order></author><author><firstname>Samuel K</firstname><surname>Sheppard</surname><order>48</order></author></authors><documents><document><filename>72176__37062__1a62e6c7a8bf4048bffb65c0b43a6189.pdf</filename><originalFilename>bmjopen-2025-109566.pdf</originalFilename><uploaded>2026-06-26T14:57:45.4363864</uploaded><type>Output</type><contentLength>1556336</contentLength><contentType>application/pdf</contentType><version>Version of Record</version><cronfaStatus>true</cronfaStatus><documentNotes>&#xA9; Author(s) (or their employer(s)) 2026. 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spelling 2026-06-26T15:03:14.8323028 v2 72176 2026-06-26 Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa be98847c72c14a731c4a6b7bc02b3bcf 0000-0002-5527-4709 Matthew Hitchings Matthew Hitchings true false 2026-06-26 MEDS 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. Journal Article BMJ Open 16 6 e109566 BMJ Publishing Group 2044-6055 0 0 0 0001-01-01 10.1136/bmjopen-2025-109566 Protocol COLLEGE NANME Medical School COLLEGE CODE MEDS Swansea University Another institution paid the OA fee This work was supported by the UK Research and Innovation Medical Research Council (MR/L015080/1, MR/T030062/1, MR/V001213/1, MC_UU_00031/1). 2026-06-26T15:03:14.8323028 2026-06-26T14:57:45.4514112 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Biomedical Science Henry Badji 1 Ben Pascoe 0000-0001-6376-5121 2 Madison P Goforth 3 Evangelos Mourkas 4 Evariste Bako 5 Isidore JO Bonkoungou 6 Modeste T Gampene 7 Marguerite Edith Malatala Nikiema 8 Barthélemy S Zoma 9 Ousman E Bah 10 Eustacia Jane Cassell 11 Abdoulie K Ceesay 12 Bubacarr E Ceesay 13 Ousman Ceesay 14 Bakary Conteh 15 Lamin Drammeh 16 Binta Faye 17 Abdoulie F Jallow 18 Fatima Jallow 19 Ousman Jallow 20 Samba Juma Jallow 21 Pa Modou Joof 22 Modou Kandeh 23 Mehrab Karim 24 Jarra Manneh 25 Abdou Ceesay 26 Ebrima Fofana 27 Mamud Jallow 28 Modou B Jarju 29 Samba Bah 30 Dodou Sanyang 31 Demba B Jallow 32 Mukaila I Alebiosu 33 Atanyiwoen Brusah 34 Akosua Bonsu Karikari 35 Courage KS Saba 36 Kaisa Haukka 37 C Matilda (Tilly) Collins 38 Adrian W Leach 39 Polina Levontin 40 Shani UP Ali 41 Frances M Colles 42 Matthew Hitchings 0000-0002-5527-4709 43 Martin Antonio 44 Abdul Karim Sesay 45 Ozan Gundogdu 46 M Jahangir Hossain 0000-0002-8415-3180 47 Samuel K Sheppard 48 72176__37062__1a62e6c7a8bf4048bffb65c0b43a6189.pdf bmjopen-2025-109566.pdf 2026-06-26T14:57:45.4363864 Output 1556336 application/pdf Version of Record true © Author(s) (or their employer(s)) 2026. This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license. true eng https://creativecommons.org/licenses/by/4.0/
title Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa
spellingShingle Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa
Matthew Hitchings
title_short Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa
title_full Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa
title_fullStr Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa
title_full_unstemmed Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa
title_sort Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa
author_id_str_mv be98847c72c14a731c4a6b7bc02b3bcf
author_id_fullname_str_mv be98847c72c14a731c4a6b7bc02b3bcf_***_Matthew Hitchings
author Matthew Hitchings
author2 Henry Badji
Ben Pascoe
Madison P Goforth
Evangelos Mourkas
Evariste Bako
Isidore JO Bonkoungou
Modeste T Gampene
Marguerite Edith Malatala Nikiema
Barthélemy S Zoma
Ousman E Bah
Eustacia Jane Cassell
Abdoulie K Ceesay
Bubacarr E Ceesay
Ousman Ceesay
Bakary Conteh
Lamin Drammeh
Binta Faye
Abdoulie F Jallow
Fatima Jallow
Ousman Jallow
Samba Juma Jallow
Pa Modou Joof
Modou Kandeh
Mehrab Karim
Jarra Manneh
Abdou Ceesay
Ebrima Fofana
Mamud Jallow
Modou B Jarju
Samba Bah
Dodou Sanyang
Demba B Jallow
Mukaila I Alebiosu
Atanyiwoen Brusah
Akosua Bonsu Karikari
Courage KS Saba
Kaisa Haukka
C Matilda (Tilly) Collins
Adrian W Leach
Polina Levontin
Shani UP Ali
Frances M Colles
Matthew Hitchings
Martin Antonio
Abdul Karim Sesay
Ozan Gundogdu
M Jahangir Hossain
Samuel K Sheppard
format Journal article
container_title BMJ Open
container_volume 16
container_issue 6
container_start_page e109566
institution Swansea University
issn 2044-6055
doi_str_mv 10.1136/bmjopen-2025-109566
publisher BMJ Publishing Group
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Biomedical Science{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Biomedical Science
document_store_str 1
active_str 0
description 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.
published_date 0001-01-01T05:42:38Z
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score 11.110217

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