Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa

Foodborne diseases (FBDs) remain a major public health concern in low- and middle-income countries (LMICs), with the African region carrying the heaviest burden globally. Surveillance efforts in these settings often overlook rural and resource-limited communities, limiting our understanding of pathogens transmission dynamics in these settings. In this study, we use whole-genome sequencing (WGS) and metagenomic approaches to characterize enteric pathogens from human, animal, and environmental sources across four African LMICs between 2019 and 2023. We analyze 446 bacterial isolates of Salmonella, Shigella, Escherichia coli, and Campylobacter, of which 380 high-quality genomes were subjected to phylogenetic and genotypic analyses. Additionally, 139 of 168 metagenomic samples pass quality control and were assessed for pathogen abundance and diversity. Our results reveal a geographically stable distribution of foodborne pathogens over time, suggesting persistent ecological or infrastructural factors influencing their maintenance. Genomic comparisons also identify closely related isolates across distinct sources and regions, pointing to potential transmission routes. These findings highlight the value of incorporating targeted environmental and food-chain sampling into surveillance strategies and demonstrate that metagenomic sequencing can serve as a practical and informative addition to WGS-based surveillance in resource-limited settings.

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Publication Details

Journal
Nature Communications
Published
2025-11-28
DOI
https://doi.org/10.1038/s41467-025-66400-9
Citations
2
Primary Topic
Salmonella and Campylobacter epidemiology
Type
article
Field-Weighted Citation Impact
2.32

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article

Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa

Olanrewaju Emmanuel Fayemi, Cecilie Thystrup, Sara M. Pires, Gabriel Bidemi Akanni et al.
2 citations
Nature Communications
Salmonella and Campylobacter epidemiology
2.32
article

Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa

Olanrewaju Emmanuel Fayemi, Cecilie Thystrup, Sara M. Pires, Gabriel Bidemi Akanni, Dinaol Belina Kitila, Kate M. Thomas, Ephrasia Hugho, Sara Lino Faife, Tosin Ogunbiyi, Happiness Kumburu, Patrick Murigu Kamau Njage, Elsa Maria Salvador, Josphat Njenga Gichure, Elna M. Buys, Tine Hald, Bélisario Moiane, Tesfaye Gobena, Christianah Idowu Ayolabi, Blandina Theophil Mmbaga
article en
2 citations

Abstract

Foodborne diseases (FBDs) remain a major public health concern in low- and middle-income countries (LMICs), with the African region carrying the heaviest burden globally. Surveillance efforts in these settings often overlook rural and resource-limited communities, limiting our understanding of pathogens transmission dynamics in these settings. In this study, we use whole-genome sequencing (WGS) and metagenomic approaches to characterize enteric pathogens from human, animal, and environmental sources across four African LMICs between 2019 and 2023. We analyze 446 bacterial isolates of Salmonella, Shigella, Escherichia coli, and Campylobacter, of which 380 high-quality genomes were subjected to phylogenetic and genotypic analyses. Additionally, 139 of 168 metagenomic samples pass quality control and were assessed for pathogen abundance and diversity. Our results reveal a geographically stable distribution of foodborne pathogens over time, suggesting persistent ecological or infrastructural factors influencing their maintenance. Genomic comparisons also identify closely related isolates across distinct sources and regions, pointing to potential transmission routes. These findings highlight the value of incorporating targeted environmental and food-chain sampling into surveillance strategies and demonstrate that metagenomic sequencing can serve as a practical and informative addition to WGS-based surveillance in resource-limited settings.

Nature CommunicationsVol. 16(1)
Haramaya University (ET), Eduardo Mondlane University (MZ), University of Lagos (NG), Moshi Co-operative University (TZ), Mountain Top University (NG), Kilimanjaro Christian Medical Centre (TZ), Pamoja Tunaweza Women's Centre (TZ), Instituto Superior de Ciencias de Saude (MZ), University of Pretoria (ZA), University of Otago (NZ), Technical University of Denmark (DK)
Bill and Melinda Gates Foundation, Foreign, Commonwealth and Development Office
Openalex Percentile: Top 10%
Salmonella and Campylobacter epidemiology
2.32
DOIOpen Access PDFOpenAlex
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