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PRJNA1391538 SRP706523

Gut resistome in pediatric HCT recipients, USA, longitudinal

Pre-HCT Resistome Disruption Predicts ESBL Gene Expansion in Pediatric Transplant Recipients: A Prospective Multi-Center Study

1242 gut metagenome samples from pediatric allogeneic hematopoietic cell transplant recipients and controls at centers in Seattle and Memphis, USA, examining multidrug-resistant organism gene dynamics in a longitudinal, multi-center design. machine-written summary

1,242 samples · 1,242 runs · US, IT · Child · 2026 · 5.75 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 13,621○Abstract / description–Full text–Supplementary tables–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive13,621 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region)
○ Abstract / descriptionread; no usable statement
– Full textno open-access full text linked
– Supplementary tablesno supplementary tables available (or none open access)
– 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
3 sampling locations · 2 countries
Age
child602
infant378
adolescent199
neonate45
adult18
Condition
other_cancer488
healthy_control446
transplant_or_immunocompromised308
Sex
male449
female332
Country
US1,139
IT103
Body site
primary1,242
Collected 2012–2023
2012: 446 samples2014: 488 samples2015: 2 samples2016: 45 samples2017: 52 samples2018: 52 samples2019: 54 samples2022: 24 samples2023: 79 samples20122023
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 17 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 1 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 2 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 10 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 112 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 917 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 182 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 1 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 5.75 Gbp per sample0130Gbp
! Self-contradictory metadata

age: two sequence archives disagree for 50 samples (e.g. 0.0 vs 121.7) — withheld.

The sources disagree on 50 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 (40 of 50)
samplefieldvalueother valuehandling
SAMN60750105age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750106age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750107age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750108age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750109age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750110age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750111age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750112age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750113age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750114age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750115age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750116age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750117age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750118age0.0 (sequence archive)121.7 (sequence archive)withheld: neither value published
SAMN60750131age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750132age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750133age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750134age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750135age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750136age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750137age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750138age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750139age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750140age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750141age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750142age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750143age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750144age18.0 (sequence archive)182.6 (sequence archive)withheld: neither value published
SAMN60750180age39.0 (sequence archive)395.7 (sequence archive)withheld: neither value published
SAMN60750181age39.0 (sequence archive)395.7 (sequence archive)withheld: neither value published
SAMN60750182age39.0 (sequence archive)395.7 (sequence archive)withheld: neither value published
SAMN60750183age39.0 (sequence archive)395.7 (sequence archive)withheld: neither value published
SAMN60750184age39.0 (sequence archive)395.7 (sequence archive)withheld: neither value published
SAMN60750185age39.0 (sequence archive)395.7 (sequence archive)withheld: neither value published
SAMN60750186age39.0 (sequence archive)395.7 (sequence archive)withheld: neither value published
SAMN60750187age39.0 (sequence archive)395.7 (sequence archive)withheld: neither value published
SAMN60750229age60.8 (sequence archive)608.7 (sequence archive)withheld: neither value published
SAMN60750230age67.0 (sequence archive)669.6 (sequence archive)withheld: neither value published
SAMN60750231age67.0 (sequence archive)669.6 (sequence archive)withheld: neither value published
SAMN60750232age67.0 (sequence archive)669.6 (sequence archive)withheld: neither value published
Sampling design and relatedness

longitudinal — not resolved

How longitudinal and relatedness information is derived

Community composition

No Sandpiper profile for this project's samples yet.

Field coverage
fieldsamplescoverageR1R2R3R4
age_category1,242 100%
country1,242 100%1,242
health_condition1,242 100%1,242
subject_id1,242 100%1,242
collection_date1,242 100%1,242
health_condition_detail1,242 100%1,242
latitude1,242 100%1,242
longitude1,242 100%1,242
detailed_location1,139 92%
location_locality1,139 92%1,139
location_region1,139 92%1,139
age_at_collection_days1,088 88%1,088
sex781 63%781
timepoint_label780 63%780
Papers (1)
  • Pre-HCT Resistome Disruption Predicts ESBL Gene Expansion in Pediatric Transplant Recipients: A Prospective Multi-Center Study 2026 own_data
Details
Archive description

Infections remain an important cause of morbidity and mortality in pediatricallogeneic hematopoietic cell transplantation (HCT) recipients. Disruption of the gut microbiota has been linked to poor outcomes in single-center studies of these patients, however application to other centers has been limited. This multi-center study aimed to evaluate drivers of multi drug resistant organism gene dynamics in pediatric HCT recipients across multiple centers in the United States and Europe.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of child and infant / toddler and adolescent by sonnet_x2 with confidence 0.68. Assay shotgun_dna.

  • host run.scientific_name · “human gut metagenome”
  • body site run.scientific_name · “human gut metagenome”
  • life stage study.title · “Pediatric Transplant Recipients”
  • life stage sample.attr.age · “1 (n=238/1242)”
  • life stage sample.attr.age · “14 (n=159/1242)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN60596371age_at_collection_days163.0R10.85sample.attr.age0.44626968
SAMN60596371collection_date2023-01-13R10.90biosample.attribute:collection_date2023-01-13
SAMN60596371countryITR10.90sample.attr.geo_loc_nameItaly: Europe
SAMN60596371health_conditiontransplant_or_immunocompromisedR10.90biosample_attrEuropean HCT
SAMN60596371health_condition_detailEuropean HCTR10.85biosample.attribute:cohortcohort: European HCT
SAMN60596371latitude42.5000R10.90biosample.attribute:lat_lon42.50 N 12.50 E
SAMN60596474location_localityMemphisR10.85biosample.attribute:geo_loc_nameUSA: Memphis
SAMN60596474location_regionTennesseeR10.60biosample.attribute:lat_lon35.1536 N 90.0435 W
SAMN60596371longitude12.5000R10.90biosample.attribute:lat_lon42.50 N 12.50 E
SAMN60596371sexmaleR10.90sample.attr.gendermale
SAMN60596371subject_id3129945R10.85sample.attr.sid3129945
SAMN60596371timepoint_labelNeutrophil_EngraftmentR10.85sample.attr.tpNeutrophil_Engraftment
Sequencing

1,242 runs over 1,242 samples · mean 6.42 Gbp per run (median 5.75 Gbp, total 7,977.59 Gbp; 1,242 runs with a base count) · layout PAIRED 1,242 · platform ILLUMINA 1,242 · models Illumina MiSeq (1,242) · 0% of runs with a Sandpiper profile · first public 2026-06-06 – 2026-06-13

Authors (0)

No author record.

Downloads

PRJNA1391538.csv.gz (38.5 KB) · parquet (126.7 KB) — all 1,242 samples, every field with route and confidence · PRJNA1391538_determinations.csv.gz (86.3 KB) — 13,621 evidence rows

Samples (1,242 · every field this project has values for · hover a cell for its source)
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