Dutch travelers' gut resistome before and after travel
614 fecal samples from 190 Dutch adults, elderly, and infants in Amsterdam, Maastricht, or Rotterdam, collected before and after international travel in a longitudinal study of gut antimicrobial resistance gene acquisition. machine-written summary
614 samples · 614 runs · NL · Adult · 2021 · 1.18 Gbp / sample · cohort Destination shapes antibiotic resistance gene acqu
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 6,296 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, latitude) |
| ✓ Abstract / description | 844 sample values (health condition, health condition detail) |
| ✓ Full text | 12 sample values (antibiotic exposure) · PMC8182900, PMC8993065 |
| ○ 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 |
age: two sequence archives disagree for 4 samples (e.g. 58.0 vs 21487.7) — withheld.
The sources disagree on 4 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN17171395 | age | 58.0 (sequence archive) | 21487.7 (sequence archive) | withheld: neither value published |
| SAMN17171396 | age | 58.0 (sequence archive) | 21487.7 (sequence archive) | withheld: neither value published |
| SAMN17171441 | age | 56.2 (sequence archive) | 20523.0 (sequence archive) | withheld: neither value published |
| SAMN17171442 | age | 56.2 (sequence archive) | 20523.0 (sequence archive) | withheld: neither value published |
longitudinal — not resolved
190 of 190 people sampled more than once (380 samples; median 2, up to 2 per person). Schedule stated by the source: “pre-travel and post-travel fecal samples (2 timepoints)” (time origin: travel_departure).
Genera, mean relative abundance over 338 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 | 614 | 100% | ||||
| country | 614 | 100% | 614 | |||
| health_condition | 614 | 100% | 4 | 610 | ||
| subject_id | 380 | 62% | 380 | |||
| antibiotic_exposure | 614 | 100% | 602 | 12 | ||
| collection_date | 614 | 100% | 614 | |||
| detailed_location | 614 | 100% | ||||
| health_condition_detail | 614 | 100% | 380 | 234 | ||
| latitude | 614 | 100% | 614 | |||
| location_region | 614 | 100% | 614 | |||
| longitude | 614 | 100% | 614 | |||
| timepoint_label | 614 | 100% | 614 | |||
| sex | 380 | 62% | 380 | |||
| age_at_collection_days | 376 | 61% | 376 | |||
| bmi | 372 | 61% | 372 | |||
| medication | 118 | 19% | 118 |
- Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers. 2021 PMID 34092249 PMC8182900 own_data
- Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli. 2022 PMID 35388735 PMC8993065 own_data
Archive description
Understand effects of travel on the gut resistome.
How this project entered the registry
Classified as human gut / stool mixed assays of adult by sonnet_x2 with confidence 0.57. Assay mixed.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “effects of travel on the gut resistome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17171223 | age_at_collection_days | 25675.0 | R1 | 0.70 | sample.attr.age | 70.2943189596167 |
| SAMN17171223 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | No |
| SAMN17171241 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | consumed antibiotics in the 3 months before travel |
| SAMN17171223 | bmi | 20.55 | R1 | 0.90 | sample.attr.bmi | 20.5498866213151 |
| SAMN17171223 | collection_date | 2012-11/2013-11 | R1 | 0.90 | biosample.attribute:collection_date | 2012-11/2013-11 |
| SAMN17171223 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands: Amsterdam, Maastricht, or Rotterdam |
| SAMN17171483 | health_condition | other_disease | R1 | 0.60 | biosample_attr | Yes |
| SAMN17171223 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | before and after travel to diverse international locations |
| SAMN17171223 | health_condition_detail | chronic gi disease: no | R1 | 0.85 | sample.attr.chronic_gi_disease | No |
| SAMN17804153 | health_condition_detail | international travelers visiting Africa or Asia | R4 | 0.50 | paper.abstract | before and after travel to diverse international locations |
| SAMN17171223 | latitude | 52.3676 | R1 | 0.90 | biosample.attribute:lat_lon | 52.3676 N 4.9041 E |
| SAMN17171223 | location_region | North Holland | R1 | 0.60 | biosample.attribute:lat_lon | 52.3676 N 4.9041 E |
| SAMN17171223 | longitude | 4.9041 | R1 | 0.90 | biosample.attribute:lat_lon | 52.3676 N 4.9041 E |
| SAMN17171243 | medication | other_medication | R1 | 0.90 | biosample.attribute:ant_diarrhoeal_drug_use | Yes |
| SAMN17171285 | medication | corticosteroid | R1 | 0.90 | biosample.attribute:corticosteroid_use | Yes |
| SAMN17171223 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN17171223 | subject_id | S003 | R1 | 0.85 | sample.attr.subject_id | S003 |
| SAMN17171223 | timepoint_label | Pre-travel | R1 | 0.85 | sample.attr.timepoint | Pre-travel |
Sequencing
614 runs over 614 samples · mean 1.08 Gbp per run (median 1.18 Gbp, total 662.60 Gbp; 614 runs with a base count) · layout PAIRED 614 · platform ILLUMINA 614 · models NextSeq 500 (614) · 55% of runs with a Sandpiper profile · first public 2021-03-29
Authors (33)
D'Souza AW first · Boolchandani M · Patel S · Galazzo G · van Hattem JM · Arcilla MS · Melles DC · de Jong MD · Schultsz C · COMBAT Consortium · Dantas G · Penders J last · Davies M first · Wolffs P · McNally A · Schaik WV · Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last
Downloads
PRJNA688274.csv.gz (17.6 KB) · parquet (96.3 KB) — all 614 samples, every field with route and confidence · PRJNA688274_determinations.csv.gz (46.2 KB) — 7,152 evidence rows