FMT for CPE gut carriage decolonization, Paris, France
68 fecal metagenome samples from CPE-colonized patients and donors in Paris, France, studying fecal microbiota transplantation (FMT) for carbapenemase-producing Enterobacterales decolonization; prospective multi-center intervention study. machine-written summary
68 samples · 68 runs · FR · Age unknown · 2024 · 3.87 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 448 sample values (collection date, country, intervention, latitude, location locality, location region, longitude, subject id) |
| ✓ Abstract / description | 136 sample values (health condition, health condition detail) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
intervention — arms not resolved
Faecal microbiota transplantation design single_arm_before_after · population gi_infection_or_diarrhoea · Single dose FMT from healthy donor for CPE decolonization
“single dose of FMT from one of four healthy donors” — abstract:38964511 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
4 of 4 people sampled more than once (21 samples; median 5, up to 7 per person) · follow-up median 3 mo (max 7 mo) · median interval between samples 14 d (time from collection dates). Schedule stated by the source: “Stool sampled before FMT and after FMT, with primary endpoint at 2 weeks and secondary endpoint at 3 months post-FMT” (time origin: intervention_start); stated follow-up 3 mo.
Each row is one person (4 shown); dots are samples at days since that person's first sample.
Recipients received FMT from one of four healthy donors; donor and recipient stool both sequenced.
Genera, mean relative abundance over 61 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 | 68 | 100% | 68 | |||
| health_condition | 68 | 100% | 68 | |||
| subject_id | 21 | 31% | 21 | |||
| collection_date | 68 | 100% | 68 | |||
| detailed_location | 68 | 100% | ||||
| health_condition_detail | 68 | 100% | 68 | |||
| latitude | 68 | 100% | 68 | |||
| location_locality | 68 | 100% | 68 | |||
| location_region | 68 | 100% | 68 | |||
| longitude | 68 | 100% | 68 | |||
| timepoint_label | 10 | 15% | 10 | |||
| intervention | 9 | 13% | 9 |
- Bacterial diversity and specific taxa are associated with decolonization of carbapenemase-producing enterobacterales after fecal microbiota transplantation. 2024 PMID 38964511 own_data
Archive description
Human fecal metagenomic sequences from the FEDEX clinical study.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host study.description · “Human fecal metagenomic sequences”
- body site study.description · “Human fecal metagenomic sequences”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN41824405 | collection_date | 2018-04-05 | R1 | 0.90 | biosample.attribute:collection_date | 2018-04-05 |
| SAMN41824405 | country | FR | R1 | 0.90 | sample.attr.geo_loc_name | France: Paris |
| SAMN41824405 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | paper.abstract | CPE-colonized patients |
| SAMN41824405 | health_condition_detail | carbapenemase-producing Enterobacterales carriage; FMT intervention cohort | R4 | 0.50 | paper.abstract | CPE-colonized patients |
| SAMN41824410 | intervention | fmt | R1 | 0.70 | sample.name_rule:alias | alias: AS-FEDEX-018-Pre_S6 |
| SAMN41824405 | latitude | 48.8575 | R1 | 0.90 | biosample.attribute:lat_lon | 48.8575 N 2.3514 E |
| SAMN41824405 | location_locality | Paris | R1 | 0.85 | biosample.attribute:geo_loc_name | France: Paris |
| SAMN41824405 | location_region | Ile-de-France | R1 | 0.60 | biosample.attribute:lat_lon | 48.8575 N 2.3514 E |
| SAMN41824405 | longitude | 2.3514 | R1 | 0.90 | biosample.attribute:lat_lon | 48.8575 N 2.3514 E |
| SAMN41824405 | subject_id | AS-FEDEX-018 | R1 | 0.70 | sample.name_rule:alias | alias: AS-FEDEX-018-040518-1_S14 |
| SAMN41824409 | timepoint_label | 90D-Post | R1 | 0.70 | sample.name_rule:alias | alias: AS-FEDEX-018-90D-Post_S10 |
Sequencing
68 runs over 68 samples · mean 4.85 Gbp per run (median 3.87 Gbp, total 329.85 Gbp; 68 runs with a base count) · layout PAIRED 68 · platform ILLUMINA 68 · models NextSeq 500 (68) · 90% of runs with a Sandpiper profile · first public 2024-07-12
Authors (13)
Davido B first · Watson AR · de Truchis P · Galazzo G · Dinh A · Batista R · Terveer EM · Lawrence C · Michelon H · Jobard M · Saleh-Mghir A · Kuijper EJ · Caballero S last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1121295.csv.gz (3.1 KB) · parquet (74.6 KB) — all 68 samples, every field with route and confidence · PRJNA1121295_determinations.csv.gz (5.1 KB) — 584 evidence rows