Fecal microbiome in CDI patients, CRS3123 vs vancomycin trial
74 fecal samples from USA and Canada patients with C. difficile infection, part of a Phase II antibiotic intervention trial comparing CRS3123 to vancomycin. machine-written summary
74 samples · 74 runs · US, CA · Age unknown · 2026 · 5.99 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 544 sample values (antibiotic exposure, collection date, country, health condition, intervention, intervention detail, subject id, timepoint) |
| ✓ Abstract / description | 122 sample values (antibiotic exposure, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC12937067 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
37 people have samples in more than one arm.
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population gi_infection_or_diarrhoea · CRS3123 (200mg or 400mg BID) vs vancomycin for C. difficile infection
“CRS3123 for treatment of C. difficile infection” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
37 of 37 people sampled more than once (74 samples; median 2, up to 2 per person) · follow-up median 12 d (max 14 d) · median interval between samples 12 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Visits: Screen, D1 (day 1), TOC (day 12 up to day 15); further clinical follow-up to day 40/70 but metagenome visit field lists only Screen/D1/TOC” (time origin: intervention_start); stated follow-up 2 mo.
Each row is one person (36 shown of 37); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 74 | 100% | 74 | |||
| health_condition | 74 | 100% | 74 | |||
| subject_id | 74 | 100% | 74 | |||
| antibiotic_exposure | 74 | 100% | 26 | 48 | ||
| collection_date | 74 | 100% | 74 | |||
| health_condition_detail | 74 | 100% | 74 | |||
| intervention | 74 | 100% | 74 | |||
| intervention_detail | 74 | 100% | 74 | |||
| timepoint_label | 74 | 100% | 74 |
- Safety and efficacy of CRS3123 in adults with a primary episode or first recurrence of Clostridioides difficile infection: a phase 2, randomised, double-blind, multicentre, vancomycin-controlled study. 2026 PMID 41581516 PMC12937067 own_data
Archive description
CRS3123 is a novel narrow-spectrum antibiotic that inhibits the methionyl-tRNA synthetase of Clostridioides difficile (CdMetRS). Safety and efficacy of CRS3123 for treatment of C. difficile infection (CDI) were recently demonstrated in a Phase II trial, with high clinical cure rates and lower recurrence compared to vancomycin. CRS3123 is highly selective for Type 1 MetRS, which has a limited phylogenetic distribution among gut bacteria compared to Type 2 MetRS. We defined Type 1-specific features of CRS3123 target binding, including cooperativity with ATP and a pronounced induced fit compared to apo CdMetRS. To examine how predicted taxonomic susceptibility may shape microbiome responses in vivo and relate to observed clinical trends, we analyzed the fecal microbiome, metabolome, and soluble immune factors from trial samples. Both 200 mg and 400 mg BID doses of CRS3123 caused less disruption of the commensal microbiome compared to vancomycin (125 QID), with less compositional deviation from external healthy controls. CRS3123 preserved Bifidobacterium and Bacteroides while effectively clearing C. difficile and vancomycin-resistant enterococci (VRE) and reducing fecal inflammatory markers. In contrast, vancomycin shifted communities toward Enterobacteriaceae. Shotgun metagenomics and targeted metabolomics showed that CRS3123- treated microbiomes retained the capacity to produce lithocholic acid, a secondary bile acid that suppresses C. difficile, whereas vancomycin promoted accumulation of conjugated primary bile acids that enhance germination. Overall, CRS3123 matches vancomycin in CDI resolution while better preserving key taxa and metabolites that may reduce CDI recurrence.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.description · “fecal microbiome, metabolome, and soluble immune factors from trial samples”
- body site study.description · “fecal microbiome, metabolome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA122609489 | antibiotic_exposure | yes | R1 | 0.85 | biosample_attr | Vancomycin_125mg_po_qid |
| SAMEA122609479 | antibiotic_exposure | yes | R4 | 0.50 | study.title | CRS3123 vs Vancomycin Treatment of CDI |
| SAMEA122609479 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMEA122609479 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA122609479 | health_condition | gi_infection_or_diarrhoea | R1 | 0.70 | biosample_attr | CRS3123_200mg_po_bid |
| SAMEA122609479 | health_condition_detail | adults with a primary episode or first recurrence of Clostridioides difficile infection | R4 | 0.50 | paper.abstract | adults with a primary episode or first recurrence of Clostridioides difficile infection |
| SAMEA122609479 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:visit | visit: D1 |
| SAMEA122609480 | intervention | antibiotic | R1 | 0.90 | biosample.attribute:treatment_group | treatment_group: CRS3123_200mg_po_bid |
| SAMEA122609479 | intervention_detail | day 1 (pre-dose baseline); assigned arm: CRS3123 200 mg orally bid | R1 | 0.80 | biosample.attribute:visit | visit: D1 |
| SAMEA122609480 | intervention_detail | CRS3123 200 mg orally bid | R1 | 0.90 | biosample.attribute:treatment_group | treatment_group: CRS3123_200mg_po_bid |
| SAMEA122609479 | subject_id | 101-1001 | R1 | 0.85 | sample.attr.host_subject_id | 101-1001 |
| SAMEA122609479 | timepoint_label | D1 | R1 | 0.85 | sample.attr.visit | D1 |
Sequencing
74 runs over 74 samples · mean 5.55 Gbp per run (median 5.99 Gbp, total 410.58 Gbp; 74 runs with a base count) · layout PAIRED 74 · platform ILLUMINA 74 · models Illumina NovaSeq X Plus (74) · 0% of runs with a Sandpiper profile · first public 2026-05-19 – 2026-05-20
Authors (0)
No author record.
Downloads
PRJEB112905.csv.gz (3.3 KB) · parquet (74.1 KB) — all 74 samples, every field with route and confidence · PRJEB112905_determinations.csv.gz (5.0 KB) — 666 evidence rows