Preterm infant gut antibiotic resistance, Hershey, PA
Cross-sectional study of 46 gut metagenome samples from preterm infants in Hershey, Pennsylvania, USA, examining antibiotic resistance. machine-written summary
46 samples · 46 runs · US · Infant / toddler · 2020 · 3.65 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 138 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 92 sample values (location site, preterm status) · PMC8827105 |
| ✓ Supplementary tables | 539 sample values (age, antibiotic exposure, birth weight grams, delivery mode, diet, family id, family role, feeding mode) |
| – 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 |
twins
5 preterm twin pairs among 46 infants (Supplementary Data 'Pair'/'Twin'); zygosity not given · 5 families with 10 sampled people, 10 twin sets.
twin · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 5 linked groups from explicit relations. 46 people in the project overall.
Families (5)
| family | members | samples |
|---|---|---|
| -10026 | twin×2 | SAMN11394104 · SAMN11394105 |
| -10029 | twin×2 | SAMN11394107 · SAMN11394108 |
| -10070 | twin×2 | SAMN11394115 · SAMN11394116 |
| -12044 | twin×2 | SAMN11394120 · SAMN11394121 |
| -2078 | twin×2 | SAMN11394079 · SAMN11394080 |
Genera, mean relative abundance over 44 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 | 46 | 100% | ||||
| country | 46 | 100% | 46 | |||
| health_condition | 46 | 100% | 46 | |||
| subject_id | 46 | 100% | 46 | |||
| age_at_collection_days | 46 | 100% | 46 | |||
| antibiotic_exposure | 46 | 100% | 46 | |||
| birth_weight_grams | 46 | 100% | 46 | |||
| collection_date | 46 | 100% | 46 | |||
| delivery_mode | 46 | 100% | 46 | |||
| detailed_location | 46 | 100% | ||||
| feeding_mode | 46 | 100% | 46 | |||
| gestational_age_weeks | 46 | 100% | 46 | |||
| health_condition_detail | 46 | 100% | 46 | |||
| location_site | 46 | 100% | 46 | |||
| maternal_antibiotics | 46 | 100% | 46 | |||
| nec_status | 46 | 100% | 46 | |||
| preterm_status | 46 | 100% | 46 | |||
| sex | 46 | 100% | 46 | |||
| diet | 13 | 28% | 13 | |||
| family_id | 10 | 22% | 10 | |||
| family_role | 10 | 22% | 10 |
- Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. PMID 34677583 PMC8827105 curated
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488 curated
Archive description
Preterm infant gut antibiotic resistance
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 · “Infant gut metagenome”
- body site study.description · “Preterm infant gut antibiotic resistance”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant gut metagenome”
- life stage study.description · “Preterm infant gut antibiotic”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11394077 | age_at_collection_days | 239 | R2 | 0.75 | paper.supp.table | Age (days)=238.98000000000002 |
| SAMN11394077 | antibiotic_exposure | yes | R2 | 0.75 | paper.supp.table | Antibiotics=True |
| SAMN11394077 | birth_weight_grams | 2200 | R2 | 0.75 | paper.supp.table | Birth_Weight(kg)=2.2 |
| SAMN11394077 | collection_date | 2016-01-01 | R1 | 0.85 | biosample.attribute:collection_date | 2016-01-01 |
| SAMN11394077 | country | US | R1 | 0.90 | biosample_attr | USA: Hershey, Pensylvania |
| SAMN11394077 | delivery_mode | c_section | R2 | 0.75 | paper.supp.table | Delivery Method=c-section |
| SAMN11394080 | diet | exclusive_breast_milk | R2 | 0.75 | paper.supp.Supplementary_tables_comb.xlsx[Supplementary Data 1!Description_of_Feeds] | 02078-BB: Description_of_Feeds=Donor milk |
| SAMN11394079 | family_id | -2078 | R2 | 0.85 | paper.supp.nqab353_supplemental_files.zip/Supplementary_tables_comb.xlsx[Supplementary Data 3!Pair] | ID 02078-BA; Twin y; Pair -2078 |
| SAMN11394079 | family_role | twin | R2 | 0.85 | paper.supp.nqab353_supplemental_files.zip/Supplementary_tables_comb.xlsx[Supplementary Data 3!Twin] | ID 02078-BA; Twin y; Pair -2078 |
| SAMN11394077 | feeding_mode | mixed | R2 | 0.75 | paper.supp.table | Nutrition=mixed-fed |
| SAMN11394077 | gestational_age_weeks | 34.14 | R2 | 0.75 | paper.supp.table | Gest_age(weeks)=34.14 |
| SAMN11394077 | health_condition | preterm_nicu | R2 | 0.80 | paper.supp.nqab353_supplemental_files.zip::Supplementary_tables_comb.xlsx[Supplementary Data 1][Inf_Inf] | N |
| SAMN11394077 | health_condition_detail | N | R2 | 0.80 | paper.supp.nqab353_supplemental_files.zip::Supplementary_tables_comb.xlsx[Supplementary Data 1][Inf_Inf] | N |
| SAMN11394077 | location_site | Penn State Hershey Medical Center NICU | R3 | 0.70 | paper.fulltext.methods | admitted to the Penn State Hershey NICU |
| SAMN11394077 | maternal_antibiotics | no | R2 | 0.75 | paper.supp.table | Mat_AB=N |
| SAMN11394077 | nec_status | no | R2 | 0.75 | paper.supp.table | NEC=False |
| SAMN11394077 | preterm_status | preterm | R3 | 0.40 | paper.fulltext.other | preterm infant gut antibiotic resistance |
| SAMN11394077 | sex | male | R2 | 0.75 | paper.supp.table | Gender=M |
| SAMN11394077 | subject_id | 01045-B | R1 | 0.85 | biosample_attr | 01045-B |
Sequencing
46 runs over 46 samples · mean 3.26 Gbp per run (median 3.65 Gbp, total 150.12 Gbp; 46 runs with a base count) · layout PAIRED 46 · platform ILLUMINA 46 · models NextSeq 500 (46) · 96% of runs with a Sandpiper profile · first public 2020-04-21
Authors (19)
Pärnänen KMM first · Hultman J · Markkanen M · Satokari R · Rautava S · Lamendella R · Wright J · McLimans CJ · Kelleher SL · Virta MP last · Lugli GA first · Mancabelli L · Milani C · Fontana F · Tarracchini C · Alessandri G · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA532310.csv.gz (3.1 KB) · parquet (74.3 KB) — all 46 samples, every field with route and confidence · PRJNA532310_determinations.csv.gz (9.0 KB) — 769 evidence rows