FMT for ESBL-Producing Enterobacteriaceae Carriers, Netherlands
79 samples from an intervention study in the Netherlands testing fecal microbiota transplantation (FMT) to decolonize patients carrying ESBL-producing Enterobacteriaceae. machine-written summary
79 samples · 178 runs · NL · Age unknown · 2022 · 5.53 Gbp / sample · cohort Drivers and determinants of strain dynamics follow
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 379 sample values (collection date, country, latitude, longitude, timepoint) |
| ✓ Abstract / description | 158 sample values (health condition, health condition detail) |
| ✓ Full text | 158 sample values (location locality, location site) · PMC10424414, PMC5863815, PMC9499871 |
| ✓ Supplementary tables | 79 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 single_arm_before_after · population gi_infection_or_diarrhoea · Fecal microbiota transplantation for ESBL-EB decolonization
“treated 15 patients carrying ESBL-producing Enterobacteriaceae” — abstract:29566738 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
16 of 16 people sampled more than once (79 samples; median 4, up to 10 per person) · follow-up median 3 mo (max 11 mo) · median interval between samples 21 d (time from collection dates). Schedule stated by the source: “day 0, 7, 14, 28 and 84 after FMT” (time origin: transplant).
Each row is one person (16 shown); dots are samples at days since that person's first sample.
16 FMT donor stool samples (donors G and P by name) and 15 recipients; donor-recipient links only via shared FMT-number token (not committed).
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 | 0 | 0% | ||||
| country | 79 | 100% | 79 | |||
| health_condition | 79 | 100% | 79 | |||
| subject_id | 79 | 100% | 79 | |||
| collection_date | 79 | 100% | 79 | |||
| detailed_location | 79 | 100% | ||||
| health_condition_detail | 79 | 100% | 79 | |||
| latitude | 79 | 100% | 79 | |||
| location_locality | 79 | 100% | 79 | |||
| location_site | 79 | 100% | 79 | |||
| longitude | 79 | 100% | 79 | |||
| timepoint_label | 63 | 80% | 63 |
- Fecal microbiota transplantation against intestinal colonization by extended spectrum beta-lactamase producing Enterobacteriaceae: a proof of principle study. 2018 PMID 29566738 PMC5863815 own_data
- Drivers and determinants of strain dynamics following fecal microbiota transplantation. 2022 PMID 36109636 PMC9499871 unsure
- Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans. 2023 PMID 37580821 PMC10424414 unsure
Archive description
Longitudinal metagenomic sequencing data for a proof-of-principle study of Fecal Microbiota Transplantation to alleviate intestinal colonization by extended-spectrum beta lactamase (ESBL) producing Enterobacteriaceae. For a detailed sample description, see Singh et al, 2018 (PMID: 29566738).
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 run.scientific_name · “human gut metagenome”
- body site study.title · “intestinal colonization by extended-spectrum beta lactamase”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA9457703 | collection_date | 2015-07-10 | R1 | 0.90 | biosample.attribute:collection_date | 2015-07-10 |
| SAMEA9457703 | country | NL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Netherlands |
| SAMEA9457703 | health_condition | other_infection | R4 | 0.50 | paper.abstract | 15 patients carrying ESBL-producing Enterobacteriaceae |
| SAMEA9457703 | health_condition_detail | All 15 patients colonized with extended-spectrum beta-lactamase producing Enterobacteriaceae. | R4 | 0.50 | paper.abstract | 15 patients carrying ESBL-producing Enterobacteriaceae |
| SAMEA9457703 | latitude | 52.1326 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.1326 5.2913 |
| SAMEA9457703 | location_locality | Amsterdam | R3 | 0.70 | paper.fulltext.methods | conducted at the Academic Medical Center (Amsterdam) |
| SAMEA9457703 | location_site | Academic Medical Center (Amsterdam) | R3 | 0.70 | paper.fulltext.methods | conducted at the Academic Medical Center (Amsterdam) |
| SAMEA9457703 | longitude | 5.2913 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.1326 5.2913 |
| SAMEA9457703 | subject_id | D_G | R2 | 0.80 | archive | |
| SAMEA9457719 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:library_names | EBS_001-11-0-0 |
| SAMEA9457797 | timepoint_label | day 0 | R1 | 0.70 | sample.name_rule:run.library_name | EBS_021A-11-0-0 |
Sequencing
178 runs over 79 samples · mean 2.44 Gbp per run (median 1.04 Gbp, total 434.45 Gbp; 178 runs with a base count) · layout PAIRED 89, SINGLE 89 · platform ILLUMINA 178 · models Illumina HiSeq 4000 (178) · 90% of runs with a Sandpiper profile · first public 2022-04-28
Authors (38)
Singh R first · de Groot PF · Geerlings SE · Hodiamont CJ · Belzer C · Berge IJMT · de Vos WM · Bemelman FJ · Nieuwdorp M last · Schmidt TSB first · Li SS · Maistrenko OM · Akanni W · Coelho LP · Dolai S · Fullam A · Glazek AM · Hercog R · Herrema H · Jung F · Kandels S · Orakov A · Thielemann R · von Stetten M · Van Rossum T · Benes V · Borody TJ · Ponsioen CY · Bork P last · Shtossel O first · Turjeman S · Riumin A · Goldberg MR · Elizur A · Bekor Y · Mor H · Koren O · Louzoun Y last
Downloads
PRJEB46779.csv.gz (3.6 KB) · parquet (74.8 KB) — all 79 samples, every field with route and confidence · PRJEB46779_determinations.csv.gz (6.5 KB) — 774 evidence rows