Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time.
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Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time.
Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.
237: Tracing enteric pathogens in Africa with metagenomics and WGS
Base by Base
20 minutes
2 weeks ago
237: Tracing enteric pathogens in Africa with metagenomics and WGS
️ Episode 237: Tracing enteric pathogens in Africa with metagenomics and WGS
In this episode of PaperCast Base by Base, we explore This study combines whole-genome sequencing and metagenomics to map the diversity, abundance, and genomic relationships of enteric foodborne pathogens across human, animal, food and environmental samples in four African LMICs
Study Highlights:The project sampled 3,417 items across Ethiopia, Mozambique, Nigeria and Tanzania between 2019 and 2023 and applied culture-based WGS and metagenomic sequencing. Of 446 recovered isolates, 380 high-quality genomes were analyzed (207 E. coli, 138 Salmonella spp., 24 Campylobacter spp., 11 Shigella spp.), and 139 metagenomes passed QC for community profiling. Pathogen distributions were geographically stable over time, with genomic clustering showing closely related isolates across distinct sources consistent with potential transmission routes. Metagenomics revealed dominant genera such as Escherichia, Enterococcus and Bifidobacterium, recovered 13 high-quality MAGs (12 E. coli, 1 Campylobacter), and provided complementary population-level insights though MAGs rarely reached strain-level identity with cultured isolates.
Conclusion:Combining targeted environmental and food-chain sampling with WGS and metagenomic sequencing strengthens surveillance and source-tracing of foodborne enteric pathogens in resource-limited African settings
Music:Enjoy the music based on this article at the end of the episode.
Reference:Thystrup C, Gobena T, Salvador EM, Fayemi OE, Kumburu H, Buys EM, Gichure J, Moiane BT, Belina D, Hugho EA, Faife S, Ogunbiyi TS, Akanni G, Ayolabi CI, Mmbaga B, Thomas KM, Pires SM, Njage PMK, Hald T. Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa. Nat Commun (2025). https://doi.org/10.1038/s41467-025-66400-9
License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/
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On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.
Keywords: metagenomics, whole-genome sequencing, foodborne pathogens, one-health, surveillance
Base by Base
Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time.
Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.
