Infant gut resistome, antibiotics and delivery mode, Ireland
209 samples from infants in Co. Cork, Ireland, collected over five early-life time points, studying effects of antibiotic use and delivery mode on gut resistome and microbial profiles; longitudinal cohort design. machine-written summary
209 samples · 209 runs · IE · Infant / toddler · 2023 · 1.50 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 834 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 209 sample values (preterm status) · PMC10837951 |
| ○ 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design observational_with_procedure · Benzylpenicillin and gentamicin exposure in first 4 days of life
“benzylpenicillin and gentamicin is associated” — abstract:38310316 (study level; per-sample arms are in the intervention column below)
longitudinal
45 of 47 people sampled more than once (206 samples; median 5, up to 5 per person) · follow-up median 24 mo (max 24 mo) · median interval between samples 28 d (time from timepoint labels). Schedule stated by the source: “week1, week4, week8, week 24, year2” (time origin: birth); stated follow-up 2.0 y.
Each row is one person (36 shown of 45); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 195 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 | 209 | 100% | ||||
| country | 209 | 100% | 209 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 208 | 100% | 208 | |||
| collection_date | 209 | 100% | 209 | |||
| preterm_status | 209 | 100% | 209 | |||
| timepoint_label | 208 | 100% | 208 |
- Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome. PMID 38310316 PMC10837951 curated
Archive description
This study includes 208 samples from 45 infants over five time points including week1, week4, week8, week 24 and year2. We analysed the effect of antibiotic use in early life and mode of delivery on resistome and microbial profiles.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- 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 · “samples from 45 infants over five time”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN35056612 | collection_date | 2012 | R1 | 0.85 | biosample.attribute:collection_date | 2012 |
| SAMN35056612 | country | IE | R1 | 0.90 | biosample_attr | Ireland: Co. Cork |
| SAMN35056612 | preterm_status | term | R3 | 0.75 | paper.fulltext.methods | full-term infants from two study cohorts |
| SAMN35056612 | subject_id | I01 | R1 | 0.70 | sample.name_rule:library_ID | I01w1 |
| SAMN35056612 | timepoint_label | week 1 | R1 | 0.70 | sample.name_rule:library_ID | I01w1 |
Sequencing
209 runs over 209 samples · mean 1.59 Gbp per run (median 1.50 Gbp, total 332.80 Gbp; 209 runs with a base count) · layout PAIRED 209 · platform ILLUMINA 209 · models NextSeq 500 (209) · 93% of runs with a Sandpiper profile · first public 2023-06-05
Authors (7)
Patangia DV first · Grimaud G · O'Shea CA · Ryan CA · Dempsey E · Stanton C · Ross RP last
Downloads
PRJNA971895.csv.gz (6.8 KB) · parquet (78.3 KB) — all 209 samples, every field with route and confidence · PRJNA971895_determinations.csv.gz (7.6 KB) — 1,043 evidence rows