Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa

Aquillah M Kanzi; Stella I Smith; Chisomo Msefula; John Mwaba; Abraham Ajayi; Geoffrey Kwenda; Collins K Tanui; Anthony M Smith; Linda A Bester; Firehiwot A Derra; Kaunda Yamba; Daniel L Banda; John B Kalule; Happiness H Kumburu; Yasmina J Fakim; Nyasha Sithole; Patrick M K Njage; Francis F Chikuse; Pascale Ondoa; Sofonias K Tessema; Ebenezer Foster-Nyarko

doi:10.1016/j.ebiom.2024.105500

Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa

EBioMedicine. 2024 Dec 18:111:105500. doi: 10.1016/j.ebiom.2024.105500. Online ahead of print.

Authors

Aquillah M Kanzi¹, Stella I Smith², Chisomo Msefula³, John Mwaba⁴, Abraham Ajayi², Geoffrey Kwenda⁵, Collins K Tanui⁶, Anthony M Smith⁷, Linda A Bester⁸, Firehiwot A Derra⁹, Kaunda Yamba¹⁰, Daniel L Banda¹¹, John B Kalule¹², Happiness H Kumburu¹³, Yasmina J Fakim¹⁴, Nyasha Sithole⁶, Patrick M K Njage¹⁵, Francis F Chikuse¹⁶, Pascale Ondoa¹⁷, Sofonias K Tessema⁶, Ebenezer Foster-Nyarko¹⁸

Affiliations

¹ African Society for Laboratory Medicine, Johannesburg, South Africa; School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu Natal, South Africa. Electronic address: [email protected].
² Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria.
³ Pathology Department, Kamuzu University of Health Sciences, Blantyre, Malawi.
⁴ Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia; Institute of Basic and Biomedical Sciences, Levy Mwanawasa Medical University, Zambia.
⁵ Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia.
⁶ Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia.
⁷ Centre for Enteric Diseases, Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa; Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
⁸ Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu Natal, South Africa; Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, South Africa.
⁹ Food Safety and Food Microbiology National Reference Laboratory, Food Science and Nutrition Research Directorate, Ethiopian Public Health Institute, Ethiopia.
¹⁰ University Teaching Hospitals, Zambia; Zambia National Public Health Institute, Zambia.
¹¹ Department of Medical Laboratory Sciences, School of Life Sciences & Allied Health Professions, Kamuzu University of Health Sciences, Malawi.
¹² Makerere University, College of Veterinary Medicine Animal Resources and Biosecurity (CoVAB), Biotechnical and Diagnostic Sciences, Uganda.
¹³ Kilimanjaro Clinical Research Institute, Tanzania; Kilimanjaro Christian Medical Centre, Tanzania; Kilimanjaro Christian Medical University College, Tanzania.
¹⁴ University of Mauritius, Mauritius.
¹⁵ Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Denmark.
¹⁶ Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia. Electronic address: [email protected].
¹⁷ African Society for Laboratory Medicine, Johannesburg, South Africa.
¹⁸ Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom.

PMID: 39700896
DOI: 10.1016/j.ebiom.2024.105500

Abstract

The role of genomics in public health surveillance has been accentuated by its crucial contributions during the COVID-19 pandemic, demonstrating its potential in addressing global disease outbreaks. While Africa has made strides in expanding multi-pathogen genomic surveillance, the integration into foodborne disease (FBD) surveillance remains nascent. Here we highlight the critical components to strengthen and scale-up the integration of whole genome sequencing (WGS) in foodborne disease surveillance across the continent. We discuss priority use-cases for FBD, and strategies for the implementation. We also highlight the major challenges such as data management, policy and regulatory frameworks, stakeholder engagement, the need for multidisciplinary collaborations and the importance of robust monitoring and evaluation, aiming to bolster Africa's preparedness and response to future health threats.

Keywords: Africa; Food-borne diseases; Genomic surveillance; Pathogen genomics; Public health; Whole-genome sequencing.

Publication types

Review