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PRJNA1148144 SRP526733

Febrile infants with extraintestinal infection: gut

Biosignatures of late-onset extraintestinal bacterial infections

24 gut metagenome samples from febrile term infants and neonates across 10 US children's hospitals, studying biosignatures linked to late-onset extraintestinal bacterial infections, using a case-control design. machine-written summary

114 samples · 114 runs · US · Infant / toddler · 2025 · 2.84 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 505○Abstract / description✓Full text 252✓Supplementary tables 120–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive505 sample values (age, country, health condition, health condition detail, sex, subject id)
○ Abstract / descriptionread; no usable statement
✓ Full text252 sample values (antibiotic exposure, collection date, preterm status) · PMC11931804, PMC13402684
✓ Supplementary tables120 sample values (health condition, health condition detail)
– 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
adult50
infant33
neonate22
adolescent7
child2
Condition
healthy_control74
sepsis_or_infection40
Sex
male63
female51
Country
US114
Body site
primary114
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 9 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 56 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 47 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 2 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 2.84 Gbp per sample0130Gbp
! Self-contradictory metadata

age: two sequence archives disagree for 59 samples (e.g. 26.0 vs 9496.5) — withheld.

The sources disagree on 59 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 59)
samplefieldvalueother valuehandling
SAMN43217629age26.0 (sequence archive)9496.5 (sequence archive)withheld: neither value published
SAMN43217630age46.0 (sequence archive)16791.5 (sequence archive)withheld: neither value published
SAMN43217632age34.0 (sequence archive)12417.9 (sequence archive)withheld: neither value published
SAMN43217638age17.0 (sequence archive)6205.8 (sequence archive)withheld: neither value published
SAMN43217641age28.0 (sequence archive)10234.0 (sequence archive)withheld: neither value published
SAMN43217643age23.0 (sequence archive)8391.0 (sequence archive)withheld: neither value published
SAMN43217645age27.0 (sequence archive)9857.0 (sequence archive)withheld: neither value published
SAMN43217647age20.0 (sequence archive)7305.0 (sequence archive)withheld: neither value published
SAMN43217649age8.0 (sequence archive)2922.0 (sequence archive)withheld: neither value published
SAMN43217650age44.0 (sequence archive)16069.0 (sequence archive)withheld: neither value published
SAMN43217655age27.0 (sequence archive)9857.0 (sequence archive)withheld: neither value published
SAMN43217656age22.0 (sequence archive)8035.5 (sequence archive)withheld: neither value published
SAMN43217658age52.0 (sequence archive)18993.0 (sequence archive)withheld: neither value published
SAMN43217663age42.0 (sequence archive)15330.0 (sequence archive)withheld: neither value published
SAMN43217664age54.0 (sequence archive)19706.0 (sequence archive)withheld: neither value published
SAMN43217667age42.0 (sequence archive)15330.0 (sequence archive)withheld: neither value published
SAMN43217670age37.0 (sequence archive)13504.0 (sequence archive)withheld: neither value published
SAMN43217675age44.0 (sequence archive)16069.0 (sequence archive)withheld: neither value published
SAMN43217676age27.0 (sequence archive)9857.0 (sequence archive)withheld: neither value published
SAMN43217677age46.0 (sequence archive)16791.5 (sequence archive)withheld: neither value published
SAMN43217678age54.0 (sequence archive)19706.0 (sequence archive)withheld: neither value published
SAMN43217680age34.0 (sequence archive)12417.9 (sequence archive)withheld: neither value published
SAMN43217681age33.0 (sequence archive)12043.2 (sequence archive)withheld: neither value published
SAMN43217682age15.0 (sequence archive)5479.0 (sequence archive)withheld: neither value published
SAMN43217683age20.0 (sequence archive)7305.0 (sequence archive)withheld: neither value published
SAMN43217685age33.0 (sequence archive)12043.2 (sequence archive)withheld: neither value published
SAMN43217686age20.0 (sequence archive)7305.0 (sequence archive)withheld: neither value published
SAMN43217688age57.0 (sequence archive)20820.0 (sequence archive)withheld: neither value published
SAMN43217690age58.0 (sequence archive)21177.0 (sequence archive)withheld: neither value published
SAMN43217693age29.0 (sequence archive)10601.0 (sequence archive)withheld: neither value published
SAMN43217694age17.0 (sequence archive)6205.8 (sequence archive)withheld: neither value published
SAMN43217696age17.0 (sequence archive)6205.8 (sequence archive)withheld: neither value published
SAMN43217697age54.0 (sequence archive)19706.0 (sequence archive)withheld: neither value published
SAMN43217701age27.0 (sequence archive)9857.0 (sequence archive)withheld: neither value published
SAMN43217702age19.0 (sequence archive)6939.0 (sequence archive)withheld: neither value published
SAMN43217703age47.0 (sequence archive)17151.0 (sequence archive)withheld: neither value published
SAMN43217704age26.0 (sequence archive)9496.5 (sequence archive)withheld: neither value published
SAMN43217706age27.0 (sequence archive)9857.0 (sequence archive)withheld: neither value published
SAMN43217707age28.0 (sequence archive)10234.0 (sequence archive)withheld: neither value published
SAMN43217708age19.0 (sequence archive)6939.0 (sequence archive)withheld: neither value published
Community composition
Streptococcus 16.0%Escherichia 12.8%Bifidobacterium 12.5%Veillonella 5.5%Staphylococcus 3.9%Klebsiella 3.4%Mediterraneibacter 3.1%Finegoldia 3.0%Phocaeicola 2.9%Enterococcus_B 2.9%Lactobacillus 2.8%Megasphaera 2.5%not assigned to a genus 3.1%other genera 25.6%

Genera, mean relative abundance over 24 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category114 100%
country114 100%114
health_condition114 100%5460
subject_id114 100%114
antibiotic_exposure114 100%114
collection_date114 100%114
health_condition_detail114 100%5460
sex114 100%114
age_at_collection_days55 48%55
preterm_status24 21%24
Papers (3)
  • Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome. PMID 40128855 PMC11931804 curated
  • An ubiquitous antibacterial toxin from human gut bacteria engenders neonatal colonization advantage. PMID 42259839 PMC13402684 curated
  • Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome. 2025 PMID 40128855 PMC11931804 own_data
Details
Archive description

Identifying gut metagenomic features associated with extraintestinal bacterial infections in febrile term infants.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult and adolescent by deterministic_prior with confidence 0.90. Assay shotgun_dna.

  • host external_curation.infant_catalog · “infant triage verdict include”
  • body site study.description · “Identifying gut metagenomic features associated”
  • body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
  • life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
  • life stage study.description · “in febrile term infants .”
  • life stage sample.attr.host_age · “27 (n=71/90)”
  • life stage sample.attr.host_age · “17 (n=9/90)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN43217631age_at_collection_days51.0R10.85biosample.attribute:host_agehost_age: 51
SAMN43217635age_at_collection_days17R10.70sample.attr.host_age17
SAMN43217629antibiotic_exposurenoR30.70paper.body.methodsInfants were excluded if they appeared critically ill, had received antibiotics in the preceding 48 h
SAMN43217629collection_date2016/2019R30.70paper.fulltext.abstractPediatric Emergency Care Applied Research Network from 2016 to 2019
SAMN43217629countryUSR10.90sample.attr.geo_loc_nameUSA: Children's Hospital Colorado
SAMN43217635countryUSR10.90biosample_attrUSA: St Louis Children's Hospital
SAMN43217629health_conditionsepsis_or_infectionR10.85biosample.attribute:host_grouphost_group: Case
SAMN43217630health_conditionhealthy_controlR20.75paper.supp.40168_2025_2079_MOESM1_ESM.xlsx[Participant metadata!Group]Sample 1058559_Stool_meta; Group Control
SAMN43217629health_condition_detailextraintestinal bacterial infection (EBI case; febrile infant)R10.85biosample.attribute:host_grouphost_group: Case
SAMN43217630health_condition_detailfebrile control without documented extraintestinal bacterial infectionR20.75paper.supp.40168_2025_2079_MOESM1_ESM.xlsx[Participant metadata!Group]Sample 1058559_Stool_meta; Group Control
SAMN43217635preterm_statustermR30.80paper.fulltext.methodswere excluded if... were born preterm
SAMN43217629sexmaleR10.90sample.attr.host_sexmale
SAMN43217635sexmaleR10.90biosample_attrmale
SAMN43217629subject_id1063919R10.85biosample.attribute:host_taxidhost_taxid: 1063919; title 1063919_Stool_meta
SAMN43217635subject_id1034354R10.85biosample_attr1034354
Sequencing

114 runs over 114 samples · mean 2.95 Gbp per run (median 2.84 Gbp, total 335.88 Gbp; 114 runs with a base count) · layout PAIRED 114 · platform ILLUMINA 114 · models Illumina NovaSeq 6000 (114) · 99% of runs with a Sandpiper profile · first public 2025-04-10 – 2025-04-27

Authors (18)

DeVeaux AL first · Hall-Moore C · Shaikh N · Wallace M · Burnham CD · Schnadower D · Kuppermann N · Mahajan P · Ramilo O · Tarr PI · Dantas G · Schwartz DJ last · Valguarnera E first · Tung J · Pak JJ · Russell SK · Hecht DW · Wardenburg JB last

Downloads

PRJNA1148144.csv.gz (4.7 KB) · parquet (76.4 KB) — all 114 samples, every field with route and confidence · PRJNA1148144_determinations.csv.gz (10.0 KB) — 877 evidence rows

Samples (114 · every field this project has values for · hover a cell for its source)
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