Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa

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: akanzi@aslm.org.
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: ChikuseF@africacdc.org.
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
PMCID: PMC11721509
DOI: 10.1016/j.ebiom.2024.105500

Review

Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa

Aquillah M Kanzi et al. EBioMedicine. 2025 Jan.

. 2025 Jan:111:105500.

doi: 10.1016/j.ebiom.2024.105500. Epub 2024 Dec 18.

Authors

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: akanzi@aslm.org.
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: ChikuseF@africacdc.org.
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
PMCID: PMC11721509
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.

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Conflict of interest statement

Declaration of interests The authors declare that they have no competing interests.

Figures

**Fig. 1**
Key elements for the acceleration genomic surveillance for foodborne diseases in African Public Health.

**Fig. 2**
An end-to-end design for implementing FBD genomic surveillance in Africa.

**Fig. 3**
The cross-sectorial unifying elements of national and regional FBD genomic surveillance.

**Fig. 4**
The holistic approach hinged on six pillars for developing a pan-African pathogen genomics data-sharing platform (AGARI) [apaportal.sanbi.ac.za].

See this image and copyright information in PMC

References

1. World Health Organization WHO estimates of the global burden of foodborne diseases: foodborne diseases burden epidemiology reference group 2007-2015. https://www.who.int/publications/i/item/9789241565165 [cited 2024 Jun 24]. Available from:
1. Havelaar A.H., Kirk M.D., Torgerson P.R., et al. World Health Organization global estimates and regional comparisons of the burden of foodborne disease in 2010. PLoS Med. 2015;12(12) - PMC - PubMed
1. Smith A.M. Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa. Afr J Lab Med. 2019;8(1):760. - PMC - PubMed
1. Nadon C., Walle I.V., Gerner-Smidt P., et al. PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Euro Surveill. 2017;22(23) - PMC - PubMed
1. Carleton H.A., Gerner-Smidt P. Whole-Genome sequencing is taking over foodborne disease surveillance: public health microbiology is undergoing its biggest change in a generation, replacing traditional methods with whole-genome sequencing. Microbe Mag. 2016;11(7):311–317.

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Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa

Affiliations

Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Medical