Vancomycin trial in C. difficile-colonized adults, St. Louis
82 fecal metagenome samples from adult patients in St. Louis, USA, colonized with C. difficile (NAAT-positive, toxin EIA-negative), from a randomized trial comparing oral vancomycin versus placebo. machine-written summary
82 samples · 82 runs · US · Age unknown · 2020 · 0.95 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 656 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 164 sample values (health condition, health condition detail) |
| ✓ Full text | 82 sample values (location site) · PMC13177613, PMC7845614 |
| ✓ Supplementary tables | 82 sample values (antibiotic exposure) |
| – 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population gi_infection_or_diarrhoea · Oral vancomycin vs placebo in C. difficile-colonized patients
“randomization to vancomycin” — abstract:33441409 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
12 of 12 people sampled more than once (82 samples; median 7, up to 8 per person). Schedule stated by the source: “Stool collected at enrollment (S01), day 5 (S02), day 10 (S03), week 4 (S04), and week 8 (S05)” (time origin: enrolment); stated follow-up 56 d.
Genera, mean relative abundance over 78 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 | 82 | 100% | ||||
| country | 82 | 100% | 82 | |||
| health_condition | 82 | 100% | 82 | |||
| subject_id | 82 | 100% | 82 | |||
| antibiotic_exposure | 82 | 100% | 82 | |||
| collection_date | 82 | 100% | 82 | |||
| detailed_location | 82 | 100% | ||||
| health_condition_detail | 82 | 100% | 82 | |||
| latitude | 82 | 100% | 82 | |||
| location_locality | 82 | 100% | 82 | |||
| location_region | 82 | 100% | 82 | |||
| location_site | 82 | 100% | 82 | |||
| longitude | 82 | 100% | 82 | |||
| timepoint_label | 82 | 100% | 82 |
- Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients. 2021 PMID 33441409 PMC7845614 own_data
- Pangenome-GWAS analysis of <i>Clostridioides difficile</i> resistant traits from healthcare- and non-healthcare-associated settings. 2026 PMID 41875899 PMC13177613 unsure
Archive description
Human fecal metagenomes isolates collected from patients and hospital environment
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host study.description · “Human fecal metagenomes isolates collected from patients”
- body site study.description · “Human fecal metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15562317 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.mSphere.00936-20_st001.xlsx[Sheet1!Antibiotics Randomization] | No |
| SAMN15562317 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN15562317 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: St. Louis |
| SAMN15562317 | health_condition | gi_infection_or_diarrhoea | R4 | 0.50 | paper.abstract | NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients |
| SAMN15562317 | health_condition_detail | C. difficile colonization (NAAT-positive, toxin EIA-negative) | R4 | 0.50 | paper.abstract | NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients |
| SAMN15562317 | latitude | 38.6270 | R1 | 0.90 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN15562317 | location_locality | St. Louis | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: St. Louis |
| SAMN15562317 | location_region | Missouri | R1 | 0.60 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN15562317 | location_site | Barnes Jewish Hospital | R3 | 0.70 | paper.fulltext.methods | conducted at Barnes Jewish Hospital (BJH) from November 2017 |
| SAMN15562317 | longitude | -90.1994 | R1 | 0.90 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN15562317 | subject_id | TN9 | R1 | 0.85 | sample.attr.patient | TN9 |
| SAMN15562317 | timepoint_label | 4 | R1 | 0.85 | sample.attr.timepoint | 4 |
Sequencing
82 runs over 82 samples · mean 1.04 Gbp per run (median 0.95 Gbp, total 85.51 Gbp; 82 runs with a base count) · layout PAIRED 82 · platform ILLUMINA 82 · models NextSeq 500 (82) · 95% of runs with a Sandpiper profile · first public 2020-11-13
Authors (16)
Fishbein SRS first · Hink T · Reske KA · Cass C · Struttmann E · Iqbal ZH · Seiler S · Kwon JH · Burnham CA · Dantas G · Dubberke ER last · Jara M first · Frias-De-Diego A · Petit R · Nguyen L · Lanzas C last
Downloads
PRJNA646752.csv.gz (3.0 KB) · parquet (74.2 KB) — all 82 samples, every field with route and confidence · PRJNA646752_determinations.csv.gz (6.2 KB) — 984 evidence rows