Preterm infant gut resistome and antibiotic exposure, USA
60 fecal samples from preterm infants in the USA (REASON study cohort), profiling antibiotic resistance genes and gut microbiota in relation to antibiotic exposure, in a longitudinal cohort design. machine-written summary
60 samples · 60 runs · US · Infant / toddler · 2024 · 0.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 300 sample values (antibiotic exposure, collection date, country, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 120 sample values (location site, preterm status) · PMC11542550 |
| ○ 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 |
longitudinal — not resolved
Schedule stated by the source: “Meconium sample at birth, then subsequent (later) stool sample(s) per infant; no explicit day offsets given” (time origin: birth).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 60 | 100% | 60 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 60 | 100% | 60 | |||
| collection_date | 60 | 100% | 60 | |||
| detailed_location | 60 | 100% | ||||
| health_condition_detail | 60 | 100% | 60 | |||
| location_site | 60 | 100% | 60 | |||
| preterm_status | 60 | 100% | 60 |
- Increased antibiotic resistance in preterm neonates under early antibiotic use. PMID 39373498 PMC11542550 curated
Archive description
The standard prophylactic use of antibiotics in newborns to prevent early-onset sepsis can adversely affect the neonatal gut microbiome, with potential long-term health impacts. Research into the escalating issue of antimicrobial resistance in preterm infants and antibiotic practices in neonatal intensive care units (NICUs) is limited. A deeper understanding of the effects of early antibiotic intervention on antibiotic resistance in preterm infants is crucial. This retrospective study employed metagenomic sequencing to evaluate antibiotic resistance genes (ARGs) in the meconium and subsequent stool samples of preterm infants enrolled in the Routine Early Antibiotic Use in Symptomatic Preterm Neonates (REASON) study. Microbial metagenomics was conducted using a subset of fecal samples from thirty preterm infants for taxonomic profiling and ARG identification. All preterm infants exhibited ARGs, with 175 unique ARGs identified, predominantly associated with Beta-lactam, Tetracycline, and Aminoglycoside resistance. Notably, 23% of ARGs were found in preterm infants without direct or intrapartum antibiotic exposure. Postnatal exposure to antibiotics increases the beta-lactam and tetracycline resistance. Microbial profiling revealed 774 bacterial species, with antibiotic-naive Preterm infants showing higher alpha diversity (p =0.005) in their microbiota and resistome compared to the treatment group, suggesting a more complex ecosystem. High ARG prevalence in Preterm infants was observed irrespective of direct antibiotic exposure and intensifies with age. Prolonged membrane ruptures and maternal antibiotic use during gestation and delivery are linked to alterations in the preterm infant resistome and microbiome, which are pivotal in shaping the ARG profiles in the neonatal gut.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “affect the neonatal gut microbiome, with potential”
- 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 · “resistance in preterm infants and antibiotic practices”
- life stage study.title · “Neonatal antibiotic resistance”
- life stage study.description · “of antibiotics in newborns to prevent early-onset”
- life stage study.description · “membrane ruptures and maternal antibiotic use during”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40717040 | antibiotic_exposure | yes | R1 | 0.85 | biosample_attr | yes |
| SAMN40717040 | collection_date | 2019-01-21 | R1 | 0.85 | biosample.attribute:collection_date | 2019-01-21 |
| SAMN40717040 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN40717040 | health_condition | preterm_nicu | R1 | 0.85 | biosample.attribute:env_local_scale | preterm neonate stool |
| SAMN40717040 | health_condition_detail | preterm neonate stool | R1 | 0.85 | biosample.attribute:env_local_scale | preterm neonate stool |
| SAMN40717040 | location_site | University of Florida | R3 | 0.70 | paper.fulltext.methods | was conducted from January 2017 to 2019 at the University of Florida |
| SAMN40717040 | preterm_status | preterm | R3 | 0.80 | paper.fulltext.methods | metagenomic sequencing to detect and quantify ARGs in preterm infant |
Sequencing
60 runs over 60 samples · mean 0.18 Gbp per run (median 0.19 Gbp, total 10.72 Gbp; 60 runs with a base count) · layout SINGLE 60 · platform OXFORD_NANOPORE 60 · models MinION (60) · 0% of runs with a Sandpiper profile · first public 2024-04-03
Authors (7)
Ojeda A first · Akinsuyi O · McKinley KL · Xhumari J · Triplett EW · Neu J · Roesch LFW last
Downloads
PRJNA1095378.csv.gz (2.4 KB) · parquet (72.0 KB) — all 60 samples, every field with route and confidence · PRJNA1095378_determinations.csv.gz (2.6 KB) — 420 evidence rows