Diarrhoea-associated metagenomes from four African countries
Cross-sectional study of 139 metagenomic samples linked to gastrointestinal infection or diarrhoea, collected in Tanzania, Ethiopia, Mozambique and Nigeria as part of foodborne disease surveillance. machine-written summary
87 samples · 139 runs · TZ, ET, MZ · Age unknown · 2024 · 18.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 292 sample values (collection date, country, health condition, health condition detail) |
| ✓ Abstract / description | 28 sample values (health condition, health condition detail) |
| ✓ Full text | 87 sample values (location locality) · PMC10143310, PMC10675616, PMC10793262, PMC11348558, PMC11521251, PMC11559196, PMC12722760, PMC13141023 |
| ✓ Supplementary tables | 28 sample values (health condition, health condition detail) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
families — not resolved
Diarrhoea cases with caretakers, siblings and household animals/food (One Health); sample-name codes not explained.
Genera, mean relative abundance over 126 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 87 | 100% | 87 | |||
| health_condition | 87 | 100% | 59 | 14 | 14 | |
| subject_id | 0 | 0% | ||||
| collection_date | 87 | 100% | 87 | |||
| detailed_location | 87 | 100% | ||||
| health_condition_detail | 87 | 100% | 59 | 14 | 14 | |
| location_locality | 87 | 100% | 87 |
- Enteric Pathogens Detected in Children under Five Years Old Admitted with Diarrhea in Moshi, Kilimanjaro, Tanzania. 2023 PMID 37111504 PMC10143310 own_data
- Molecular Characterization of Hetero-Pathogenic and Diarrheagenic Escherichia coli Pathotypes in Diarrheic Children under Five Years and Exposure Environment in Ogun State, South-West Nigeria. 2023 PMID 38003822 PMC10675616 own_data
- High diversity of Salmonella spp. from children with diarrhea, food, and environmental sources in Kilimanjaro - Tanzania: one health approach. 2023 PMID 38235427 PMC10793262 own_data
- Outbreak detection in Harar town and Kersa district, Ethiopia using phylogenetic analysis and source attribution. 2024 PMID 39187763 PMC11348558 own_data
- Occurrence and diversity of Campylobacter species in diarrheic children and their exposure environments in Ethiopia. 2024 PMID 39471170 PMC11521251 own_data
3 more
- Genotypic Antimicrobial Resistance Profiles of Diarrheagenic Escherichia coli and Nontyphoidal Salmonella Strains Isolated from Children with Diarrhea and Their Exposure Environments in Ethiopia. 2024 PMID 39539744 PMC11559196
- Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa. 2025 PMID 41315421 PMC12722760
- Strain-level analyses of public sequencing data to characterize <i>Escherichia coli</i> strain sharing between children and chickens in Mozambique. 2026 PMID 42094845 PMC13141023
Archive description
The "Foodborne disease epidemiology, surveillance, and Control in African LMIC"-project (FOCAL) links public-health surveillance data with pathogen occurrence data from food, animals and the environment, to provide the best evidence of the health impact of, and the relative contribution of different sources for, foodborne infections in African low- middle-income countries.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human feces metagenome”
- host run.scientific_name · “chicken gut metagenome”
- host run.scientific_name · “wastewater metagenome”
- body site run.scientific_name · “human feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA116102880 | collection_date | 2021-03-22 | R1 | 0.90 | biosample.attribute:collection_date | 2021-03-22 |
| SAMEA116102880 | country | NG | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Nigeria |
| SAMEA116102880 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:DESCRIPTION | Fecal sample from child with diarrhea |
| SAMEA116102895 | health_condition | healthy_control | R2 | 0.85 | paper.supp.41467_2025_66400_MOESM3_ESM.xlsx[Metagenome_stats!Source] | Caretaker |
| SAMEA116102901 | health_condition | gi_infection_or_diarrhoea | R4 | 0.50 | paper.abstract | children admitted with diarrhea |
| SAMEA116102880 | health_condition_detail | Fecal sample from child with diarrhea | R1 | 0.85 | biosample.attribute:DESCRIPTION | Fecal sample from child with diarrhea |
| SAMEA116102895 | health_condition_detail | Caretaker | R2 | 0.85 | paper.supp.41467_2025_66400_MOESM3_ESM.xlsx[Metagenome_stats!Source] | Caretaker |
| SAMEA116102901 | health_condition_detail | Diarrhea-causing pathogens detected in 80.14% of study population | R4 | 0.50 | paper.abstract | children admitted with diarrhea |
| SAMEA116102880 | location_locality | Moshi | R3 | 0.70 | paper.fulltext.abstract | admitted with diarrhea in health facilities in Moshi, Kilimanjaro |
Sequencing
139 runs over 87 samples · mean 19.71 Gbp per run (median 18.18 Gbp, total 2,740.20 Gbp; 139 runs with a base count) · layout PAIRED 139 · platform ILLUMINA 139 · models Illumina NovaSeq X (139) · 91% of runs with a Sandpiper profile · first public 2024-09-30 – 2024-11-06
Authors (38)
Hugho EA first · Kumburu HH · Amani NB · Mseche B · Maro A · Ngowi LE · Kyara Y · Kinabo G · Thomas KM · Houpt ER · Liu J · Hald T · Mmbaga BT last · Ogunbiyi TS first · Fayemi OE · Akanni GB · Ayolabi CI · Thomas K · Lukambagire AS · Wadugu B · Amani N · Belina D first · Gobena T · Kebede A · Chimdessa M · Olson N first · Thystrup CAN · Smith F · Mucache H · Fafetine J · Saíde J · Mondlane-Milisse A · Brito DRA · Jesser KJ · Brown J · Freeman M · Levy K · Nadimpalli ML last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJEB73590.csv.gz (3.5 KB) · parquet (73.5 KB) — all 87 samples, every field with route and confidence · PRJEB73590_determinations.csv.gz (4.1 KB) — 435 evidence rows