Preterm neonate bacteremia and gut microbiome, case-control
390 stool samples from hospitalized preterm infants (birthweight ≤2000 g, postnatal age ≤2 months), comparing bacteremia cases matched to uninfected controls using whole metagenome sequencing in a case-control design. machine-written summary
390 samples · 390 runs · US · Infant / toddler · 2026 · 5.26 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 780 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 780 sample values (location site, preterm status) · PMC12316594 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
longitudinal — not resolved
Schedule stated by the source: “weekly stools collected from hospitalized preterm infants” (time origin: birth).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 390 | 100% | ||||
| country | 390 | 100% | 390 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 390 | 100% | 390 | |||
| detailed_location | 390 | 100% | ||||
| location_site | 390 | 100% | 390 | |||
| preterm_status | 390 | 100% | 390 |
- Associations between antibiotic exposure intensity, intestinal microbiome perturbations, and outcomes in premature neonates with bacteremia. PMID 40490486 PMC12316594 curated
Archive description
Neonatal microbiome dysbiosis is associated with infectious complications. Prospective weekly stools were collected over 1 year from hospitalized preterm infants with birthweight less than or equal to 2000 g and postnatal age (PNA) less than or equal to 2 months. Neonates with bacteremia cases were matched to uninfected controls. Stools were analyzed using whole metagenome sequencing. Intensity of antibiotic exposure was compared using an Antibiotic Spectrum Index (ASI). We analyzed 398 stools from 40 cases and 39 controls. Cases had lower alpha diversity beyond 4 weeks PNA. Cases with subsequent infections after index bacteremia had persistently lower alpha diversity, while cases without subsequent infections demonstrated recovery of microbiome diversity. Compared to controls, cases had greater ASI at multiple timepoints, higher Enterococcus spp. and lower anaerobe abundance. Compared to controls, premature neonates with bacteremia had intestinal microbiomes with lower alpha diversity, higher Enterococcus spp. and lower anaerobe abundance. These changes were associated with recurrent infectious complications
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “antibiotic exposure intensity, intestinal microbiome perturbations, and”
- body site study.description · “complications. Prospective weekly stools were collected over”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “from hospitalized preterm infants with birthweight less”
- life stage study.title · “and outcomes in premature neonates with bacteremia”
- life stage study.description · “Neonatal microbiome dysbiosis is”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN62014771 | collection_date | 2021-07-29 | R1 | 0.85 | biosample.attribute:collection_date | 2021-07-29 |
| SAMN62014771 | country | US | R1 | 0.90 | biosample_attr | USA: Tennessee, Nashville |
| SAMN62014771 | location_site | Vanderbilt University Medical Center NICU | R3 | 0.70 | paper.fulltext.methods | admitted to the NICU at Vanderbilt University Medical Center |
| SAMN62014771 | preterm_status | preterm | R3 | 0.60 | paper.fulltext.abstract | prospective weekly stools were collected ... from hospitalized preterm infants |
Sequencing
390 runs over 390 samples · mean 5.05 Gbp per run (median 5.26 Gbp, total 1,968.56 Gbp; 390 runs with a base count) · layout PAIRED 390 · platform ILLUMINA 390 · models Illumina NovaSeq X (390) · 0% of runs with a Sandpiper profile · first public 2026-07-30
Authors (6)
Hendricks H first · Israel S · Weitkamp JH · Pakala S · Rajagopala S · Banerjee R last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1502892.csv.gz (11.7 KB) · parquet (87.1 KB) — all 390 samples, every field with route and confidence · PRJNA1502892_determinations.csv.gz (9.9 KB) — 1,560 evidence rows