Neonatal fecal resistome after early-life antibiotics
20 fecal/rectal swab samples from neonates in the western Netherlands, shotgun-sequenced to characterize the resistome following early-life broad-spectrum antibiotic treatment versus untreated controls, within a randomized controlled trial. machine-written summary
20 samples · 32 runs · NL · Infant / toddler · 2022 · 64.7 Mbp / sample · cohort Reyman 2022 Netherlands
One study deposited as 2 BioProjects (32 catalog samples together): PRJNA613032 · PRJNA613054 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 72 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 60 sample values (age, antibiotic exposure, preterm status) · PMC8850541 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · Randomized IV antibiotics (pen+gent, co-amoxiclav+gent, or amox+cefotaxime) for sEONS vs controls
“randomized 1:1:1 to receive three commonly prescribed intravenous antibiotic combinations” — abstract:35173154 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 5 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 | 20 | 100% | ||||
| country | 20 | 100% | 20 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 12 | 60% | 12 | |||
| age_at_collection_days | 20 | 100% | 20 | |||
| antibiotic_exposure | 20 | 100% | 20 | |||
| collection_date | 20 | 100% | 20 | |||
| preterm_status | 20 | 100% | 20 | |||
| timepoint_label | 20 | 100% | 20 |
- Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial. PMID 35173154 PMC8850541 curated
Archive description
We performed a randomised controlled study in 147 infants requiring broad-spectrum antibiotic treatment for suspected early onset neonatal sepsis in their first week of life. Infants were randomly allocated to either treatment with penicillin + gentamicin, co-amoxiclav + gentamicin or amoxicillin + cefotaxime. Healthy infants not receiving antibiotics in their first week of life served as controls (subset of samples from BioProject ID PRJNA481243). Microbiota of faecal samples and rectal swabs were characterised by 16S rRNA-based sequencing (BioProject ID PRJNA612836 + BioProject ID PRJNA524461). The resistome of a subset of 32 samples collected from this cohort and the controls was additionally characterised by whole genome shotgun sequencing.
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 · “Fecal resistome in early”
- body site study.description · “PRJNA481243). Microbiota of faecal samples and rectal”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Fecal resistome in early life and effects of”
- life stage study.description · “suspected early onset neonatal sepsis in their”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09696208 | age_at_collection_days | 6 | R3 | 0.60 | paper.fulltext.results | post antibiotics and 12 controls at 1 week of age |
| SAMN09696208 | antibiotic_exposure | yes | R3 | 0.70 | paper.fulltext.abstract | requiring broad-spectrum antibiotics for treatment of sEONS |
| SAMN09696208 | collection_date | 2014-05-24 | R1 | 0.85 | biosample.attribute:collection_date | 2014-05-24 |
| SAMN09696208 | country | NL | R1 | 0.90 | biosample_attr | Netherlands: western part |
| SAMN09696208 | preterm_status | term | R3 | 0.70 | paper.fulltext.methods | healthy, term-born infants from the Dutch |
| SAMN09696208 | subject_id | 080 | R1 | 0.85 | biosample.attribute:pid | pid: 080 |
| SAMN09696208 | timepoint_label | 42 | R1 | 0.80 | biosample_attr | 42 |
| SAMN11050924 | timepoint_label | 2 | R1 | 0.85 | biosample.attribute:time | time: 2 |
Sequencing
32 runs over 32 samples · mean 80.5 Mbp per run (median 64.7 Mbp, total 2.58 Gbp; 32 runs with a base count) · layout PAIRED 32 · platform ILLUMINA 32 · models Illumina NovaSeq 6000 (32) · 0% of runs with a Sandpiper profile · first public 2022-01-12
Authors (12)
Reyman M first · van Houten MA · Watson RL · Chu MLJN · Arp K · de Waal WJ · Schiering I · Plötz FB · Willems RJL · van Schaik W · Sanders EAM · Bogaert D last
Downloads
PRJNA613054.csv.gz (1.6 KB) · parquet (70.5 KB) — all 20 samples, every field with route and confidence · PRJNA613054_determinations.csv.gz (1.8 KB) — 132 evidence rows