E. coli strain-sharing across households in Nairobi, Kenya
Cross-sectional study of 321 samples (human stool, poultry cloacal swabs, canine feces, drinking water, soil) from 50 Nairobi households, examining E. coli strain-sharing and antibiotic resistance gene overlap across humans, animals, and environment. machine-written summary
321 samples · 321 runs · KE · Age unknown · 2024 · 2.04 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,926 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12055605 |
| ✓ Supplementary tables | 524 sample values (family id, family role, shared setting id, shared setting type) |
| – 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 |
familieshouseholdsmother–infant
50 Nairobi households (48 with >=2 sampled people): 46 mothers, 52 children <5 y, 34 siblings, plus household poultry, dog, water, soil · 48 families with 130 sampled people (45 with a parent and a child) · 48 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 48 families (one per family structure, then more) · 8 of 48 shared settings.
Families (25 of 48)
Genera, mean relative abundance over 290 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 | 321 | 100% | 321 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 321 | 100% | 321 | |||
| detailed_location | 321 | 100% | ||||
| latitude | 321 | 100% | 321 | |||
| location_locality | 321 | 100% | 321 | |||
| location_region | 321 | 100% | 321 | |||
| longitude | 321 | 100% | 321 | |||
| family_id | 132 | 41% | 132 | |||
| family_role | 132 | 41% | 132 | |||
| shared_setting_id | 130 | 40% | 130 | |||
| shared_setting_type | 130 | 40% | 130 |
- Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements. 2025 PMID 40312516 PMC12055605 own_data
Archive description
To investigate strain-sharing patterns, we collected matched human stool, animal samples (poultry cloacal swabs and canine feces), and environmental samples (stored drinking water and household soil) from 50 households in Nairobi, Kenya. Using Pooling Isolated Colonies-seq (PIC-seq), we sequenced pools of up to five Escherichia coli colonies per sample to capture strain diversity, strain-sharing patterns, and the overlap of antibiotic resistance genes (ARGs) including their genomic context.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool / other human site shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.53. Assay shotgun_dna.
- host study.description · “collected matched human stool, animal samples”
- body site study.description · “collected matched human stool, animal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN41976918 | collection_date | 2019-06-20 | R1 | 0.90 | biosample.attribute:collection_date | 2019-06-20 |
| SAMN41976918 | country | KE | R1 | 0.90 | sample.attr.geo_loc_name | Kenya: Nairobi |
| SAMN41976920 | family_id | 4 | R2 | 0.85 | paper.supp.41564_2025_1986_MOESM18_ESM.xlsx[source_data_extended_data_fig_8!HH1/HH2] | sample C1004; HH 4; subcounty Kibera; host Human |
| SAMN41976920 | family_role | child | R2 | 0.70 | sample.name_rule:alias | sample C1004; 46 mothers, 52 children <5, 34 siblings |
| SAMN41976918 | latitude | -1.3143 | R1 | 0.90 | biosample.attribute:lat_lon | 1.3143398 S 36.786034 E |
| SAMN41976918 | location_locality | Nairobi | R1 | 0.85 | biosample.attribute:geo_loc_name | Kenya: Nairobi |
| SAMN41976918 | location_region | Nairobi Area | R1 | 0.60 | biosample.attribute:lat_lon | 1.3143398 S 36.786034 E |
| SAMN41976918 | longitude | 36.7860 | R1 | 0.90 | biosample.attribute:lat_lon | 1.3143398 S 36.786034 E |
| SAMN41976920 | shared_setting_id | 4 | R2 | 0.85 | paper.supp.41564_2025_1986_MOESM18_ESM.xlsx[source_data_extended_data_fig_8!HH1/HH2] | sample C1004; HH 4; subcounty Kibera; host Human |
| SAMN41976920 | shared_setting_type | household | R2 | 0.85 | paper.supp.41564_2025_1986_MOESM18_ESM.xlsx[source_data_extended_data_fig_8!HH1/HH2] | sample C1004; HH 4; subcounty Kibera; host Human |
Sequencing
321 runs over 321 samples · mean 2.11 Gbp per run (median 2.04 Gbp, total 678.76 Gbp; 321 runs with a base count) · layout PAIRED 321 · platform ILLUMINA 321 · models Illumina NovaSeq 6000 (321) · 90% of runs with a Sandpiper profile · first public 2024-09-12
Authors (8)
Kim DD first · Swarthout JM · Worby CJ · Chieng B · Mboya J · Earl AM · Njenga SM · Pickering AJ last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA1126668.csv.gz (9.4 KB) · parquet (84.5 KB) — all 321 samples, every field with route and confidence · PRJNA1126668_determinations.csv.gz (17.6 KB) — 2,450 evidence rows