PRJNA1308273 SRP656172
Gut metagenomics of E. coli ST131 carriage, Singapore cohort
ST131 gut metagenomics and Escherichia coli whole genomes
Cross-sectional shotgun metagenomics of 255 fecal samples from a Singapore cohort, examining gut microbiome features associated with E. coli ST131 gut carriage status (persistent, intermittent, non-carrier) and household transmission risk. machine-written summary
255 samples · 255 runs · SG · Age unknown · 2026 · 5.28 Gbp / sample
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Sources
✓ Sequence archive 1,785 ○ Abstract / description○ Full text✓ Supplementary tables 1,020 – External resources– User contribution– Human verified
Checked this project's papers and archive records yourself? Mark it human-verified .
what each source gave ✓ Sequence archive1,785 sample values (collection date, country, health condition detail, latitude, location locality, longitude, timepoint) ○ Abstract / descriptionread; no usable statement ○ Full textread; no usable statement or table · PMC13534727 ✓ Supplementary tables1,020 sample values (family id, family role, shared setting id, shared setting type) – External resourcesnot covered by the external resources we ingest – User contributionnothing uploaded yet · share metadata – Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Collected 2017–2018
2017: 162 samples 2018: 93 samples 2017 2018 Sequencing depth per sample ·
all projects, 0–0.03 Gbp: 25,080 samples (4 %) all projects, 0.03–0.1 Gbp: 17,066 samples (3 %) all projects, 0.1–0.3 Gbp: 29,179 samples (5 %) all projects, 0.3–1 Gbp: 47,044 samples (8 %) all projects, 1–3 Gbp: 124,983 samples (22 %) this project, 1–3 Gbp: 16 samples all projects, 3–10 Gbp: 253,728 samples (44 %) this project, 3–10 Gbp: 236 samples all projects, 10–30 Gbp: 72,533 samples (13 %) this project, 10–30 Gbp: 3 samples all projects, 30–100 Gbp: 3,024 samples (1 %) all projects, 100–300 Gbp: 106 samples (0 %) all projects, ≥ 300 Gbp: 9 samples (0 %) project median 5.28 Gbp per sample 0 1 30 Gbp
Sampling design and relatedness
longitudinal — not resolved households
Schedule stated by the source: “not specified beyond 'Baseline' and 'Repeat' timepoint labels; no stated interval”.
255 samples from 119 people in 34 households (household codes in Zenodo metadata); ST131 household transmission · 34 families with 255 sampled people · 34 shared settings.
household_member H household_member H household_member H household_member H 7 × household_member×4
household_member H household_member H household_member H household_member H household_member H household_member H 5 × household_member×6
household_member H household_member H household_member H 4 × household_member×3
household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H 4 × household_member×8
household_member H household_member H household_member H household_member H household_member H household_member H household_member H 2 × household_member×7
household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H 2 × household_member×11
household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H 2 × household_member×13
household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H household_member H 1 × household_member×10
family 11051702 family 11051702 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 2061704 family 2061704 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 11051701 family 11051701 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 11071708 family 11071708 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 17061702 family 17061702 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 20061710 family 20061710 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 22051701 family 22051701 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 11061710 family 11061710 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 13071701 family 13071701 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 14021702 family 14021702 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 18051704 family 18051704 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 23061701 family 23061701 nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 25021704 family 25021704 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 30051708 family 30051708 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 8061704 family 8061704 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 12061703 family 12061703 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 21061707 family 21061707 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 21061713 family 21061713 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 12071709 family 12071709 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 26061707 family 26061707 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 25021703 family 25021703 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 29051702 family 29051702 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 15061710 family 15061710 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan family 25051709 family 25051709 nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan nan — household member · 1 sample H nan household 30051708 · 20 people household 30051708 nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan household 13071701 · 17 people household 13071701 nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan household 8061704 · 16 people household 8061704 nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan household 29051702 · 13 people household 29051702 nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan household 22051701 · 13 people household 22051701 nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan household 25021704 · 12 people household 25021704 nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan household 20061710 · 11 people household 20061710 nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan household 25021703 · 11 people household 25021703 nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan nan — member · 1 sample nan
Families (25 of 34) How longitudinal and relatedness information is derived
Community composition
No Sandpiper profile for this project's samples yet.
Papers (1)
Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study. 2026 PMID 42680742 PMC13534727 own_data
Details
Archive description WGS of isolates from patients of different infections (e.g.Urinary tract infection , bacteremia)
How this project entered the registry Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.55. Assay shotgun_dna .
host run.host_tax_id · “9606”body site run.scientific_name · “human gut metagenome”Evidence examples (one per field × route)
sample field value route conf. source quote
SAMN54597288 collection_date 2017-08-04 R1 0.90 biosample.attribute:collection_date 2017-08-04 SAMN54597288 country SG R1 0.90 sample.attr.geo_loc_name Singapore SAMN54597288 family_id 2061704 R2 0.85 paper.supp.zenodo.20728515/metadata.xlsx[R!household] SN MHH407; subject_code 02061704A; household 2061704 SAMN54597288 family_role household_member R2 0.85 paper.supp.zenodo.20728515/metadata.xlsx[R!household] SN MHH407; subject_code 02061704A; household 2061704 SAMN54597288 health_condition_detail non_carrier R1 0.90 sample.attr.host_phenotype non_carrier SAMN54597288 latitude 1.2910 R1 0.90 biosample.attribute:lat_lon 1.291 N 103.8 E SAMN54597288 location_locality Singapore R1 0.85 biosample.attribute:geo_loc_name Singapore SAMN54597288 longitude 103.8000 R1 0.90 biosample.attribute:lat_lon 1.291 N 103.8 E SAMN54597288 shared_setting_id 2061704 R2 0.85 paper.supp.zenodo.20728515/metadata.xlsx[R!household] SN MHH407; subject_code 02061704A; household 2061704 SAMN54597288 shared_setting_type household R2 0.85 paper.supp.zenodo.20728515/metadata.xlsx[R!household] SN MHH407; subject_code 02061704A; household 2061704 SAMN54597288 timepoint_label Baseline R1 0.85 sample.attr.timepoint Baseline
Sequencing 255 runs over 255 samples · mean 5.50 Gbp per run (median 5.28 Gbp, total 1,402.61 Gbp; 255 runs with a base count) · layout PAIRED 255 · platform ILLUMINA 255 · models Illumina HiSeq 4000 (224), Illumina NovaSeq 6000 (31) · 0% of runs with a Sandpiper profile · first public 2026-06-17
Authors (15) Low A first · Yang Z · Anantaya KT · Zhao S · Tan WC · Perez RL · Chung The H · Lim SZY · Liu L · Gounot JS · Kwah JS · Ong RT · Nagarajan N · Lee JWJ · Mo Y last
Help complete this project 3 of the 4 core fields are below 50% coverage: age_category , health_condition , subject_id . Share metadata
Downloads PRJNA1308273.csv.gz (8.1 KB) · parquet (81.2 KB) — all 255 samples, every field with route and confidence · PRJNA1308273_determinations.csv.gz (19.1 KB) — 2,805 evidence rows
Samples (255 · every field this project has values for · hover a cell for its source)
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