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PRJNA528511 SRP191068

Global traveler AMR surveillance, stool isolates

Global TravEpiNet AMR surveillance Genome sequencing and assembly

Cross-sectional study of 888 samples (pre- and post-travel isolates) collected in the USA (Boston, New York, Salt Lake City) from adult international travelers, sequencing antimicrobial-resistant Enterobacterales to study global AMR gene distribution. machine-written summary

888 samples · 888 runs · US · Age unknown · 2023 · 4.33 Gbp / sample

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Sources
✓Sequence archive 4,428○Abstract / description✓Full text 12✓Supplementary tables 496–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive4,428 sample values (collection date, country, location locality, location region, subject id, timepoint)
○ Abstract / descriptionread; no usable statement
✓ Full text12 sample values (collection date) · PMC10680401, PMC12811885
✓ Supplementary tables496 sample values (sex)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 country
Age
adult888
Sex
female269
male227
Country
US888
Body site
primary888
Collected 2017–2020
2017: 17 samples2018: 621 samples2019: 245 samples2020: 5 samples20172020
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 13 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 4 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 5 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 22 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 167 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 638 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 39 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 4.33 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

299 of 366 people sampled more than once (821 samples; median 2, up to 5 per person) · follow-up median 23 d (max 23 mo) · median interval between samples 36 d (time from collection dates). Schedule stated by the source: “Pre-travel (D0) and post-travel stool samples at D14, D90, D180, and D360 for the same traveler.” (time origin: travel); stated follow-up 12 mo.

112912112912: day 0112912: day 14112912: day 112112912: day 218112912: day 393112947112947: day 0112947: day 23112947: day 135112947: day 217112947: day 397113278113278: day 0113278: day 7113278: day 109113278: day 201113278: day 383113412113412: day 0113412: day 20113412: day 101113412: day 207113412: day 390113483113483: day 0113483: day 9113483: day 111113483: day 202113483: day 376114008114008: day 0114008: day 102114008: day 208114008: day 295114008: day 512114277114277: day 0114277: day 6114277: day 108114277: day 220114277: day 410114288114288: day 0114288: day 12114288: day 108114288: day 200114288: day 401114487114487: day 0114487: day 32114487: day 84114487: day 217114487: day 394114573114573: day 0114573: day 19114573: day 116114573: day 116114573: day 367114576114576: day 0114576: day 19114576: day 121114576: day 204114576: day 386114611114611: day 0114611: day 7114611: day 110114611: day 188114611: day 378114813114813: day 0114813: day 20114813: day 113114813: day 209114813: day 392115179115179: day 0115179: day 69115179: day 166115179: day 234115179: day 447115309115309: day 0115309: day 23115309: day 127115309: day 211115309: day 443115341115341: day 0115341: day 9115341: day 112115341: day 196115341: day 384115749115749: day 0115749: day 11115749: day 111115749: day 198115749: day 378116249116249: day 0116249: day 17116249: day 123116249: day 248116249: day 408116265116265: day 0116265: day 15116265: day 125116265: day 217116265: day 392116316116316: day 0116316: day 10116316: day 142116316: day 212116316: day 384116360116360: day 0116360: day 10116360: day 131116360: day 228116360: day 398116376116376: day 0116376: day 10116376: day 145116376: day 231116376: day 426116594116594: day 0116594: day 18116594: day 133116594: day 213116594: day 384116809116809: day 0116809: day 35116809: day 204116809: day 399116809: day 712116919116919: day 0116919: day 91116919: day 161116919: day 262116919: day 542117375117375: day 0117375: day 20117375: day 115117375: day 213117375: day 392117389117389: day 0117389: day 15117389: day 121117389: day 218117389: day 379117408117408: day 0117408: day 14117408: day 85117408: day 278117408: day 384117663117663: day 0117663: day 11117663: day 111117663: day 196117663: day 391118118118118: day 0118118: day 27118118: day 154118118: day 217118118: day 398118177118177: day 0118177: day 17118177: day 116118177: day 212118177: day 382118453118453: day 0118453: day 10118453: day 116118453: day 195118453: day 375118477118477: day 0118477: day 14118477: day 141118477: day 198118477: day 385118621118621: day 0118621: day 12118621: day 110118621: day 206118621: day 384118689118689: day 0118689: day 24118689: day 114118689: day 200118689: day 458119298119298: day 0119298: day 11119298: day 86119298: day 195119298: day 3560 d6 mo12 mo18 mo23 mo

Each row is one person (36 shown of 299); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Faecalibacterium 8.9%Bacteroides 7.4%Blautia_A 6.5%Roseburia 5.7%Alistipes 5.0%Phocaeicola 4.4%Prevotella 3.2%Bifidobacterium 2.9%Gemmiger 2.5%Fusicatenibacter 2.0%Collinsella 1.8%Ruminococcoides 1.8%not assigned to a genus 6.8%other genera 41.2%

Genera, mean relative abundance over 815 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category888 100%
country888 100%888
health_condition0 0%
subject_id888 100%888
collection_date888 100%87612
detailed_location888 100%
timepoint_label888 100%888
location_locality819 92%819
sex496 56%496
location_region69 8%69
Papers (2)
  • Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis. 2023 PMID 37716364 PMC10680401 own_data
  • Insights Into Global Antimicrobial Resistance Dynamics Through the Sequencing of Enteric Bacteria From US International Travelers. 2026 PMID 40990287 PMC12811885 own_data
Details
Archive description

Global TravEpiNet AMR surveillance

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.50. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site sample.attr.isolation_source · “stool (n=888/888)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN31237109collection_date2018-01-16R10.90biosample.attribute:collection_date2018-01-16
SAMN31237361collection_date2017/2019R30.70paper.fulltext.methodsbetween 2017 and 2019
SAMN31237109countryUSR10.90sample.attr.geo_loc_nameUSA: Boston
SAMN31237109location_localityBostonR10.85biosample.attribute:geo_loc_nameUSA: Boston
SAMN31237399location_regionNew YorkR10.85biosample.attribute:geo_loc_nameUSA: New York
SAMN31237109sexmaleR20.75paper.supp.jiaf469_supplementary_data.zip::SupplementaryTables.xlsx[Table S1!gender]112535 | gender: M
SAMN31237109subject_id112535R10.70sample.name_rule:alias112535_D0
SAMN31237109timepoint_labelD0R10.70sample.name_rule:alias112535_D0
Sequencing

888 runs over 888 samples · mean 4.69 Gbp per run (median 4.33 Gbp, total 4,165.97 Gbp; 888 runs with a base count) · layout PAIRED 888 · platform ILLUMINA 888 · models Illumina NovaSeq 6000 (888) · 92% of runs with a Sandpiper profile · first public 2023-11-26 – 2025-07-27

Authors (22)

Worby CJ first · Sridhar S · Turbett SE · Becker MV · Kogut L · Sanchez V · Bronson RA · Rao SR · Oliver E · Walker AT · Walters MS · Kelly P · Leung DT · Knouse MC · Hagmann SHF · Harris JB · Ryan ET · Earl AM · LaRocque RC last · Shea T · Holliday LK · Slater D

Downloads

PRJNA528511.csv.gz (27.5 KB) · parquet (106.8 KB) — all 888 samples, every field with route and confidence · PRJNA528511_determinations.csv.gz (40.2 KB) — 4,936 evidence rows

Samples (888 · every field this project has values for · hover a cell for its source)
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