Bloodstream infections after FMT for GvHD, Israel
37 stool samples from FMT donors and recipients at two Israeli medical centers (Chaim Sheba Medical Center and Rambam Health Care Campus), studying bloodstream infection origin after fecal microbiota transplantation for graft-versus-host-disease, case-control design. machine-written summary
37 samples · 37 runs · IL · Age unknown · 2021 · 0.79 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 284 sample values (collection date, country, latitude, location locality, location region, location site, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 74 sample values (health condition, health condition detail) · PMC8791595 |
| ✓ Supplementary tables | 1 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 |
intervention — arms not resolved
Faecal microbiota transplantation design observational_with_procedure · population transplant_or_immunocompromised · Fecal microbiota transplantation for graft-versus-host-disease, donor/recipient stool screening
“bloodstream infections (BSIs) following fecal microbiota transplantation (FMT)” — abstract:34644375 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
9 of 14 people sampled more than once (31 samples; median 4, up to 5 per person) · follow-up median 30 d (max 39 d) · median interval between samples 9 d (time from collection dates). Schedule stated by the source: “Multiple stool samples per patient collected on different dates (pre/post FMT) over observation period”.
Each row is one person (6 shown of 9); dots are samples at days since that person's first sample.
FMT capsules (donor material, 10 capsules) + recipient stool and blood-culture samples from 13 patients; capsule-to-patient assignment not given (Table S4).
Genera, mean relative abundance over 33 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 | 37 | 100% | 37 | |||
| health_condition | 37 | 100% | 37 | |||
| subject_id | 37 | 100% | 36 | 1 | ||
| detailed_location | 37 | 100% | ||||
| health_condition_detail | 37 | 100% | 37 | |||
| latitude | 37 | 100% | 37 | |||
| location_locality | 37 | 100% | 37 | |||
| location_region | 37 | 100% | 37 | |||
| location_site | 37 | 100% | 37 | |||
| longitude | 37 | 100% | 37 | |||
| collection_date | 26 | 70% | 26 |
- Origins of bloodstream infections following fecal microbiota transplantation: a strain-level analysis. 2022 PMID 34644375 PMC8791595 own_data
Archive description
We observed high rates of bloodstream infections (BSIs) following fecal microbiota transplantation (FMT) for graft-versus-host-disease (33 events in 22 patients). To trace the BSIs' origin, we applied a metagenomic bioinformatic pipeline screening donor and recipient stool samples for bacteremia-causing strains in 13 cases. Offending strains were not detected in FMT donations. Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii could be detected in stool samples before emerging in the blood. In this largest report of BSIs post-FMT, we present an approach that may be applicable for evaluating BSI origin following microbiota-based interventions. Our findings support FMT safety in immunocompromised patients but do not rule out FMT as an inducer of bacterial translocation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site study.description · “donor and recipient stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21507521 | collection_date | 2017-07-09 | R1 | 0.90 | biosample.attribute:collection_date | 2017-07-09 |
| SAMN21507521 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel: Chaim Sheba Medical Center, Tal Hashomer, Ramat Gan |
| SAMN21507521 | health_condition | autoimmune_inflammatory | R3 | 0.70 | paper.fulltext.methods | steroid-resistant or steroid-dependent acute GVHD |
| SAMN21507521 | health_condition_detail | steroid-resistant/steroid-dependent acute graft-versus-host-disease (GVHD) | R3 | 0.70 | paper.fulltext.methods | steroid-resistant or steroid-dependent acute GVHD |
| SAMN21507521 | latitude | 32.0700 | R1 | 0.90 | biosample.attribute:lat_lon | 32.07 N 34.84 E |
| SAMN21507521 | location_locality | Ramat Gan | R1 | 0.85 | biosample.attribute:geo_loc_name | Israel: Chaim Sheba Medical Center, Tal Hashomer, Ramat Gan |
| SAMN21507521 | location_region | Tel Aviv | R1 | 0.60 | biosample.attribute:lat_lon | 32.07 N 34.84 E |
| SAMN21507521 | location_site | Chaim Sheba Medical Center | R1 | 0.85 | biosample.attribute:geo_loc_name | Israel: Chaim Sheba Medical Center, Tal Hashomer, Ramat Gan |
| SAMN21507521 | longitude | 34.8400 | R1 | 0.90 | biosample.attribute:lat_lon | 32.07 N 34.84 E |
| SAMN21507521 | subject_id | M001 | R1 | 0.70 | sample.name_rule:title | Stool sample for patient M001 from 09/07/2017 |
| SAMN21507546 | subject_id | R001 | R2 | 0.85 | paper.supp.advancesADV2021005110-suppl1.pdf[p6t1!Patient/ donor number] | R001 |
Sequencing
37 runs over 37 samples · mean 2.24 Gbp per run (median 0.79 Gbp, total 82.77 Gbp; 37 runs with a base count) · layout PAIRED 37 · platform ILLUMINA 37 · models Illumina HiSeq 2500 (37) · 92% of runs with a Sandpiper profile · first public 2021-11-01
Authors (13)
Eshel A first · Sharon I · Nagler A · Bomze D · Danylesko I · Fein JA · Geva M · Henig I · Shimoni A · Zuckerman T · Youngster I · Koren O · Shouval R last
Downloads
PRJNA764525.csv.gz (2.2 KB) · parquet (72.6 KB) — all 37 samples, every field with route and confidence · PRJNA764525_determinations.csv.gz (3.8 KB) — 359 evidence rows