Campylobacter in children and livestock, rural Ethiopia
Longitudinal cohort study of 177 samples from young children, adults, livestock, and environmental reservoirs in rural eastern Ethiopia, examining Campylobacter species diversity, reservoir attribution, and links to gut microbiota and child health. machine-written summary
177 samples · 263 runs · ET · Infant / toddler · 2025 · 0.35 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 818 sample values (collection date, country, family id, family role, shared setting id, shared setting type) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 531 sample values (lifestyle, lifestyle detail, location region) · PMC12581456 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
householdsmother–infantsiblings
40 households: 36 infant+mother+sibling, 3 infant+mother, 1 infant+sibling (116 human samples); household livestock also sampled · 40 families with 116 sampled people (39 with a parent and a child) · 40 shared settings.
motherchildsiblingmember · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 24 of 40 families (one per family structure, then more) · 8 of 40 shared settings.
Families (25 of 40)
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 177 | 100% | 177 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 177 | 100% | 177 | |||
| detailed_location | 177 | 100% | ||||
| lifestyle | 177 | 100% | 177 | |||
| lifestyle_detail | 177 | 100% | 177 | |||
| location_region | 177 | 100% | 177 | |||
| family_id | 116 | 66% | 116 | |||
| family_role | 116 | 66% | 116 | |||
| shared_setting_id | 116 | 66% | 116 | |||
| shared_setting_type | 116 | 66% | 116 |
- Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia. PMID 41185061 PMC12581456 curated
Archive description
The project seeks to understand the livestock reservoirs for Campylobacter infection. It aims to gain insight into Campylobacter species composition, genomic diversity, and its presence in livestock and how they are related to these bacteria in the gut of young children. The study addresses the following objectives,</p><p>1) Assess the prevalence, species composition, and genomic diversity of thermotolerant and non-thermotolerant Campylobacter species in young children, adults, livestock, and other reservoirs in the rural area of eastern Ethiopia</p><p>2) Determine the attribution of Campylobacter infections in young children to humans, livestock, and other reservoirs (i.e. drinking water, soil) based on the genetic population structure of Campylobacter species circulating in these reservoirs</p><p>3) Assess associations among the presence of Campylobacter species, gut microbiota, and the health status of children
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “bacteria in the gut of young children.”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “gut of young children . The study”
- life stage study.description · “in young children, adults , livestock, and”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN46308608 | collection_date | 2021-01-12 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2021-01-12 |
| SAMN46308608 | country | ET | R1 | 0.90 | biosample_attr | Ethiopia |
| SAMN46308612 | family_id | HH028 | R1 | 0.70 | biosample.attribute:source_material_id | source_material_id=028HM01 |
| SAMN46308612 | family_role | mother | R1 | 0.85 | biosample.attribute:isolation_source | isolation_source=Mother stool |
| SAMN46308608 | lifestyle | rural_non_industrialized | R3 | 0.70 | paper.fulltext.methods | 10 rural kebeles (synonymous with villages) of Haramaya woreda |
| SAMN46308608 | lifestyle_detail | Rural farming households with co-habiting livestock | R3 | 0.60 | paper.fulltext.methods | 10 rural kebeles (synonymous with villages) of Haramaya woreda |
| SAMN46308608 | location_region | Oromia Region | R3 | 0.70 | paper.fulltext.methods | East Hararghe Zone, Oromia Region, Ethiopia |
| SAMN46308612 | shared_setting_id | HH028 | R1 | 0.70 | biosample.attribute:source_material_id | source_material_id=028HM01 |
| SAMN46308612 | shared_setting_type | household | R1 | 0.70 | biosample.attribute:source_material_id | source_material_id=028HM01 |
Sequencing
263 runs over 177 samples · mean 0.34 Gbp per run (median 0.35 Gbp, total 90.30 Gbp; 263 runs with a base count) · layout PAIRED 263 · platform ILLUMINA 263 · models NextSeq 2000 (263) · 0% of runs with a Sandpiper profile · first public 2025-01-24 – 2025-02-02
Authors (37)
Terefe Y first · Deblais L · Ghanem M · Helmy YA · Mummed B · Chen D · Singh N · Ahyong V · Kalantar K · Yimer G · Yousuf Hassen J · Mohammed A · McKune SL · Manary MJ · Ordiz MI · Gebreyes W · Havelaar AH · Rajashekara G last · Havelaar A · Yousuf J · McKune S · O'Mathúna D last · Bardosh K · Yang Y · Diaz N · Roba KT · Ketema M · Ameha N · Assefa N · Bardosh KL first · Hussein JW · Sadik EA · Hassen JY · Ibrahim AM · Mekuria Z first · Ojeda A · on behalf on the CAGED Research Team last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA843963.csv.gz (6.6 KB) · parquet (79.2 KB) — all 177 samples, every field with route and confidence · PRJNA843963_determinations.csv.gz (12.0 KB) — 1,349 evidence rows