Stool metagenomics in enteric infection patients, Winnipeg
Cross-sectional study of 304 stool samples from patients with gastrointestinal infection or diarrhoea in Winnipeg, Canada, evaluating shotgun metagenomics for detecting enteric bacterial pathogens compared to standard culture and PCR. machine-written summary
304 samples · 323 runs · CA · Age unknown · 2022 · 1.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,824 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 608 sample values (health condition, health condition detail) · PMC8880012 |
| ✓ Supplementary tables | 304 sample values (subject id) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
12 of 284 people sampled more than once (32 samples; median 2, up to 6 per person). Schedule stated by the source: “31 samples from 12 patients, average 1.4 days apart (opportunistic repeat specimens, not a fixed schedule)”.
Genera, mean relative abundance over 271 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 | 304 | 100% | 304 | |||
| health_condition | 304 | 100% | 304 | |||
| subject_id | 304 | 100% | 304 | |||
| collection_date | 304 | 100% | 304 | |||
| detailed_location | 304 | 100% | ||||
| health_condition_detail | 304 | 100% | 304 | |||
| latitude | 304 | 100% | 304 | |||
| location_locality | 304 | 100% | 304 | |||
| location_region | 304 | 100% | 304 | |||
| longitude | 304 | 100% | 304 |
- Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool. 2022 PMID 35208895 PMC8880012 own_data
Archive description
Using metagenomic data to ID enteric pathogens in stool (304 samples)
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. 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 |
|---|---|---|---|---|---|---|
| SAMN23704848 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMN23704848 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Winnipeg |
| SAMN23704848 | health_condition | gi_infection_or_diarrhoea | R3 | 0.70 | paper.fulltext.methods | 304 human stool specimens from 285 patients with lab-confirmed gastroenteritis |
| SAMN23704848 | health_condition_detail | patients with lab-confirmed gastroenteritis | R3 | 0.70 | paper.fulltext.methods | 304 human stool specimens from 285 patients with lab-confirmed gastroenteritis |
| SAMN23704848 | latitude | 49.8900 | R1 | 0.90 | biosample.attribute:lat_lon | 49.89 N 97.13 W |
| SAMN23704848 | location_locality | Winnipeg | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Winnipeg |
| SAMN23704848 | location_region | Manitoba | R1 | 0.60 | biosample.attribute:lat_lon | 49.89 N 97.13 W |
| SAMN23704848 | longitude | -97.1300 | R1 | 0.90 | biosample.attribute:lat_lon | 49.89 N 97.13 W |
| SAMN23704848 | subject_id | SAMN23704848 | R2 | 0.75 | paper.supp.microorganisms-10-00441-s001.zip/Dataset 1_Results Summary.xlsx[general data!Patient] | unique |
Sequencing
323 runs over 304 samples · mean 1.50 Gbp per run (median 1.04 Gbp, total 485.25 Gbp; 323 runs with a base count) · layout PAIRED 323 · platform ILLUMINA 323 · models Illumina MiSeq (323) · 87% of runs with a Sandpiper profile · first public 2022-05-19
Authors (12)
Peterson CL first · Alexander D · Chen JC · Adam H · Walker M · Ali J · Forbes J · Taboada E · Barker DOR · Graham M · Knox N · Reimer AR last
Downloads
PRJNA786578.csv.gz (8.4 KB) · parquet (83.6 KB) — all 304 samples, every field with route and confidence · PRJNA786578_determinations.csv.gz (18.3 KB) — 2,736 evidence rows