Base by Base23 Dec 2025

237: Tracing enteric pathogens in Africa with metagenomics and WGS

Thystrup C et al., Nat Commun (2025) - 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. Key terms: metagenomics, whole-genome sequencing, foodborne pathogens, one-health, surveillance.

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.

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

First author:
Thystrup C

Journal:
Nat Commun (2025)

DOI:
10.1038/s41467-025-66400-9

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:
CC BY 4.0 International License (CC BY 4.0)

Support:
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Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/metagenomics-wgs-africa

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-23.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript’s discussion of study design (WGS vs metagenomics), multicountry sampling, major pathogen findings (E. coli, Salmonella, Campylobacter, Shigella), STs (ST131, ST38, ST1208), MAGs and their concordance with culture data, temporal sewage trends (2021), and limitations (database bias, AMR on plasmid
- transcript topics: WGS vs metagenomics methodological comparison; FOCAL project sampling across four African LMICs; Pathogen diversity across human, animal, food, and environmental reservoirs; E. coli typing (ST131, ST38) and Salmonella typing (ST1208); MAGs and culture-independent surveillance; Temporal trends in sewage pathogen burden (2021 spike)

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- 3,417 samples coll...

Chapters

(00:00:00) - Meeting the challenges of diarrheal disease tracking
(00:05:52) - WGS findings on diarrheal disease
(00:06:53) - E. Coli, Salmonella
(00:08:01) - The wide angle lens of metagenomic science
(00:13:19) - Getting it out there: pathogens in our water
(00:14:25) - Follow the Signal

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