Gut microbiome in children treated for cellulitis, Australia
96 faecal samples from Australian children with moderate/severe cellulitis, comparing IV ceftriaxone at home versus IV flucloxacillin in hospital; part of a randomised, controlled, non-inferiority trial. machine-written summary
96 samples · 96 runs · AU · Child · 2022 · 6.65 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 480 sample values (country, latitude, longitude, subject id, timepoint) |
| ✓ Abstract / description | 288 sample values (antibiotic exposure, health condition, health condition detail) |
| – Full text | no open-access full text linked |
| – 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 · population other_infection · IV ceftriaxone at home vs IV flucloxacillin in hospital for cellulitis
“IV ceftriaxone at home compared to IV flucloxacillin in hospital” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
23 of 72 people sampled more than once (47 samples; median 2, up to 3 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 3 mo (time from timepoint labels).
Each row is one person (5 shown of 23); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 81 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 | 96 | 100% | ||||
| country | 96 | 100% | 96 | |||
| health_condition | 96 | 100% | 96 | |||
| subject_id | 96 | 100% | 96 | |||
| antibiotic_exposure | 96 | 100% | 96 | |||
| health_condition_detail | 96 | 100% | 96 | |||
| latitude | 96 | 100% | 96 | |||
| longitude | 96 | 100% | 96 | |||
| timepoint_label | 96 | 100% | 96 |
Archive description
CHOICE was a 12-month, single-centre, open-label, randomised, controlled, non-inferiority trial that aimed to investigate the safety and efficacy of IV ceftriaxone at home compared to IV flucloxacillin in hospital for treatment of moderate to severe cellulitis in children. CHOICE-Biome aimed to address the effect of these treatments on the faecal and gut microbiome, as well as the collection of antimicrobial resistance genes, known as the resistome. CHOICE-Biome used both 16S rRNA gene sequencing and deep metagenomic sequencing followed up by specific qPCR assays to investigate this.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “faecal and gut microbiome”
- life stage study.description · “moderate to severe cellulitis in children”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7049598 | antibiotic_exposure | yes | R4 | 0.50 | study.description | IV ceftriaxone at home compared to IV flucloxacillin |
| SAMEA7049598 | country | AU | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Australia |
| SAMEA7049598 | health_condition | other_infection | R4 | 0.50 | study.description | moderate to severe cellulitis in children |
| SAMEA7049598 | health_condition_detail | Cellulitis (bacterial skin infection) | R4 | 0.50 | study.description | moderate to severe cellulitis in children |
| SAMEA7049598 | latitude | -25.2744 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 25.2744� S 133.7751� E |
| SAMEA7049598 | longitude | 133.7751 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 25.2744� S 133.7751� E |
| SAMEA7049598 | subject_id | 102 | R1 | 0.70 | sample.name_rule:sample_title | 1021WST |
| SAMEA7049598 | timepoint_label | 1W | R1 | 0.60 | sample.name_rule:sample_title | 1021WST |
Sequencing
96 runs over 96 samples · mean 5.53 Gbp per run (median 6.65 Gbp, total 530.87 Gbp; 96 runs with a base count) · layout PAIRED 96 · platform ILLUMINA 96 · models HiSeq X Ten (96) · 89% of runs with a Sandpiper profile · first public 2022-12-16
Authors (0)
No author record.
Downloads
PRJEB39128.csv.gz (3.4 KB) · parquet (74.0 KB) — all 96 samples, every field with route and confidence · PRJEB39128_determinations.csv.gz (6.1 KB) — 768 evidence rows