NICU bloodstream infection gut microbiome, case-control, USA
Shotgun metagenomic sequencing of 449 samples from infants and neonates in a neonatal intensive care unit in the USA, comparing bloodstream infection cases and controls in a case-control design. machine-written summary
449 samples · 449 runs · US · Infant / toddler · 2023 · 1.23 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,570 sample values (age, birth weight grams, country, delivery mode, health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC13402684 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
subject ids shared by samples of both sexes (1 ids, 22 samples) — ids withheld.
The sources disagree on 22 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 (22)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN31008600 | subject id | 340.01 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008601 | subject id | 340.01 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008602 | subject id | 340.01 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008603 | subject id | 340.01 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008604 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008605 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008606 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008607 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008608 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008609 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008610 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008611 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008612 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008613 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008614 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008615 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008616 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008617 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008618 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008619 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008620 | subject id | 340.01 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN31008621 | subject id | 340.01 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
longitudinal
51 of 51 people sampled more than once (427 samples; median 8, up to 18 per person) · follow-up median 27 d (max 2 mo) · median interval between samples 3 d (time from age at collection).
Each row is one person (36 shown of 51); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 379 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 | 449 | 100% | ||||
| country | 449 | 100% | 449 | |||
| health_condition | 449 | 100% | 449 | |||
| subject_id | 427 | 95% | 427 | |||
| age_at_collection_days | 449 | 100% | 449 | |||
| birth_weight_grams | 449 | 100% | 449 | |||
| delivery_mode | 449 | 100% | 449 | |||
| health_condition_detail | 449 | 100% | 449 | |||
| sex | 449 | 100% | 449 |
- An ubiquitous antibacterial toxin from human gut bacteria engenders neonatal colonization advantage. PMID 42259839 PMC13402684 curated
Archive description
Shotgun metagenomic sequencing of bloodstream infection cases and controls in neonatatal intensive care unit.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of neonate and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Gut residence of bloodstream”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage study.title · “pathogens in the NICU”
- life stage study.description · “and controls in neonatatal intensive care unit.”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31008317 | age_at_collection_days | 30 | R1 | 0.90 | biosample_attr | 30 |
| SAMN31008317 | birth_weight_grams | 630 | R1 | 0.90 | biosample_attr | 630 |
| SAMN31008317 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN31008317 | delivery_mode | c_section | R1 | 0.90 | biosample_attr | caeserean |
| SAMN31008317 | health_condition | sepsis_or_infection | R1 | 0.85 | biosample.attribute:exp_type | exp_type: experimental |
| SAMN31008317 | health_condition_detail | experimental | R1 | 0.85 | biosample.attribute:exp_type | exp_type: experimental |
| SAMN31008317 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN31008317 | subject_id | 1002.01 | R1 | 0.85 | biosample_attr | 1002.01 |
Sequencing
449 runs over 449 samples · mean 1.24 Gbp per run (median 1.23 Gbp, total 558.08 Gbp; 449 runs with a base count) · layout PAIRED 449 · platform ILLUMINA 449 · models Illumina NovaSeq 6000 (449) · 85% of runs with a Sandpiper profile · first public 2023-06-05
Authors (20)
Schwartz DJ first · Shalon N · Wardenburg K · DeVeaux A · Wallace MA · Hall-Moore C · Ndao IM · Sullivan JE · Radmacher P · Escobedo M · Burnham CD · Warner BB · Tarr PI · Dantas G last · Valguarnera E first · Tung J · Pak JJ · Russell SK · Hecht DW · Wardenburg JB last
Downloads
PRJNA884103.csv.gz (14.3 KB) · parquet (89.1 KB) — all 449 samples, every field with route and confidence · PRJNA884103_determinations.csv.gz (19.0 KB) — 3,570 evidence rows