Antibiotics for travelers' diarrhea, deployed servicemembers
416 fecal samples from servicemembers deployed to Kenya or Honduras, studying travelers' diarrhea and single-dose treatment or daily prophylactic antibiotic regimens, in two clinical trials. machine-written summary
416 samples · 416 runs · KE, HN · Age unknown · 2023 · 1.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,506 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 416 sample values (antibiotic exposure) |
| ✓ Full text | 1,664 sample values (health condition, health condition detail, lifestyle, lifestyle detail) · PMC10790752 |
| ✓ Supplementary tables | 1,450 sample values (age, intervention, sex, subject id, timepoint) |
| – 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
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population gi_infection_or_diarrhoea · Single-dose antibiotic treatment regimens and rifaximin prophylaxis for travelers' diarrhea
“three single-dose antibiotic reg-imens to treat TD” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalmilitary unit — not resolved
163 of 163 people sampled more than once (416 samples; median 2, up to 6 per person) · follow-up median 35 d (max 35 d) · median interval between samples 35 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “TrEAT TD: stool at day 0 (TD onset), day 7, day 21; PREVENT TD: stool at visit 1 (pre-deployment) and visit 2 (end of deployment, ~35 days later)” (time origin: diagnosis).
Each row is one person (36 shown of 163); dots are samples at days since that person's first sample.
deployed US military servicemembers in two trials; no unit identifiers.
Genera, mean relative abundance over 373 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 | 416 | 100% | ||||
| country | 416 | 100% | 416 | |||
| health_condition | 416 | 100% | 416 | |||
| subject_id | 416 | 100% | 184 | 232 | ||
| antibiotic_exposure | 416 | 100% | 416 | |||
| collection_date | 416 | 100% | 416 | |||
| detailed_location | 416 | 100% | ||||
| health_condition_detail | 416 | 100% | 416 | |||
| latitude | 416 | 100% | 416 | |||
| lifestyle | 416 | 100% | 416 | |||
| lifestyle_detail | 416 | 100% | 416 | |||
| location_region | 416 | 100% | 416 | |||
| longitude | 416 | 100% | 416 | |||
| timepoint_label | 416 | 100% | 242 | 174 | ||
| age_at_collection_days | 406 | 98% | 406 | |||
| sex | 406 | 98% | 406 | |||
| intervention | 232 | 56% | 232 |
- Gut microbiome and antibiotic resistance effects during travelers' diarrhea treatment and prevention. 2024 PMID 38085102 PMC10790752 own_data
Archive description
We applied shotgun metagenomic and whole genome sequencing to a collection of longitu-dinally-collected fecal samples and cultured bacteria collected during two military-led clinical trials: TrEAT TD , which evaluated the effectiveness of three single-dose antibiotic reg-imens to treat TD, and PREVENT TD, which evaluated the effectiveness of the antibiotic rifaximin as a prophylaxis to prevent TD during international deployment.
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.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33781480 | age_at_collection_days | 15706 | R2 | 0.85 | paper.supp.mbio.02790-23-s0001.xlsx[Tab_2-Samples_info!AGE] | 43 |
| SAMN33781480 | antibiotic_exposure | yes | R4 | 0.50 | study.title | antibiotic regimens for the prevention and treatment |
| SAMN33781480 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMN33781480 | country | HN | R1 | 0.90 | sample.attr.geo_loc_name | Honduras |
| SAMN33781480 | health_condition | gi_infection_or_diarrhoea | R3 | 0.70 | paper.fulltext.abstract | impacts of these regimens on travelers' gut microbiomes |
| SAMN33781480 | health_condition_detail | antibiotic regimens for treatment/prevention of travelers' diarrhea | R3 | 0.70 | paper.fulltext.abstract | impacts of these regimens on travelers' gut microbiomes |
| SAMN33781664 | intervention | placebo | R2 | 0.85 | paper.supp.mbio.02790-23-s0002.xlsx[Prevent_TD_stool_clinical_data_][Randomisation] | PU0122_V1 | Randomisation: Placebo |
| SAMN33781480 | latitude | 14.0820 | R1 | 0.90 | biosample.attribute:lat_lon | 14.081999 N 87.202438 W |
| SAMN33781480 | lifestyle | military | R3 | 0.70 | paper.fulltext.methods | US servicemembers deployed to Honduras who experienced acute watery diarrhea |
| SAMN33781480 | lifestyle_detail | US and UK military servicemembers deployed overseas | R3 | 0.70 | paper.fulltext.methods | US servicemembers deployed to Honduras who experienced acute watery diarrhea |
| SAMN33781480 | location_region | Francisco Morazan | R1 | 0.60 | biosample.attribute:lat_lon | 14.081999 N 87.202438 W |
| SAMN33781480 | longitude | -87.2024 | R1 | 0.90 | biosample.attribute:lat_lon | 14.081999 N 87.202438 W |
| SAMN33781480 | sex | male | R2 | 0.85 | paper.supp.mbio.02790-23-s0001.xlsx[Tab_2-Samples_info!SEX] | Male |
| SAMN33781480 | subject_id | 0361 | R1 | 0.70 | sample.name_rule:alias | 0361-1 |
| SAMN33781664 | subject_id | PU0122 | R2 | 0.85 | paper.supp.mbio.02790-23-s0002.xlsx[Prevent_TD_stool_clinical_data_][studyid] | PU0122_V1 | studyid: PU0122 |
| SAMN33781654 | timepoint_label | V1 | R1 | 0.70 | sample.name_rule:alias | PU0100_V1 |
| SAMN33781480 | timepoint_label | 0 | R2 | 0.85 | paper.supp.mbio.02790-23-s0001.xlsx[Tab_2-Samples_info!TIMEPOINT] | 0 |
Sequencing
416 runs over 416 samples · mean 1.38 Gbp per run (median 1.18 Gbp, total 573.94 Gbp; 416 runs with a base count) · layout PAIRED 416 · platform ILLUMINA 416 · models NextSeq 550 (416) · 90% of runs with a Sandpiper profile · first public 2023-11-17 – 2023-11-26
Authors (18)
Blake KS first · Schwartz DJ · Paruthiyil S · Wang B · Ning J · Isidean SD · Burns DS · Whiteson H · Lalani T · Fraser JA · Connor P · Troth T · Porter CK · Tribble DR · Riddle MS · Gutiérrez RL · Simons MP · Dantas G last
Downloads
PRJNA945408.csv.gz (12.9 KB) · parquet (87.6 KB) — all 416 samples, every field with route and confidence · PRJNA945408_determinations.csv.gz (48.5 KB) — 6,036 evidence rows