Gut resistome in children with severe pneumonia, sub-Saharan Africa
Shotgun metagenomics of 631 peri-rectal swabs (plus 51 extraction controls) from children under 6 with severe community-acquired pneumonia in South Africa, Zambia, Zimbabwe and Uganda, from the PediCAP trial. machine-written summary
682 samples · 682 runs · ZA, UG, ZM · Age unknown · 2026 · 0.13 Gbp / sample · cohort Impact of co-amoxiclav versus amoxicillin on the g
One study deposited as 2 BioProjects (1,313 catalog samples together): PRJEB90577 · PRJNA1277853 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,206 sample values (collection date, country, latitude, location locality, longitude) |
| ✓ Abstract / description | 784 sample values (antibiotic exposure, health condition, health condition detail) |
| ✓ Full text | 1,262 sample values (health condition, health condition detail) · PMC13530132 |
| ○ 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 · share metadata |
| – 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 to continued IV antibiotics vs step-down oral amoxicillin/co-amoxiclav, varying durations
“randomized to continue IV therapy or step-down to oral amoxicillin” — abstract:42168578 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Peri-rectal swabs collected after starting IV antibiotics (randomization), at hospital discharge, and at a follow-up visit four weeks after randomization.”; stated follow-up 28 d.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 682 | 100% | 682 | |||
| health_condition | 682 | 100% | 631 | 51 | ||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 682 | 100% | 682 | |||
| health_condition_detail | 682 | 100% | 631 | 51 | ||
| collection_date | 631 | 93% | 631 | |||
| detailed_location | 631 | 93% | ||||
| latitude | 631 | 93% | 631 | |||
| location_locality | 631 | 93% | 631 | |||
| longitude | 631 | 93% | 631 |
- Impact of co-amoxiclav versus amoxicillin on the gastrointestinal microbiota in sub-Saharan children hospitalized with pneumonia. 2026 PMID 42168578 PMC13530132 own_data
Archive description
Raw reads of the samples sequenced within the PediCAP trial (RIA2017MC). Peri-rectal swabs were sequenced using a shotgun metagenomic approach on a NextSeq instrument. Nasopharyngeal swabs were sequenced using a metaserotyping approach on a MinION instrument.
How this project entered the registry
Classified as human gut / stool / nasal / nasopharyngeal / multiple sites mixed assays of age unknown by curator_audit with confidence 0.00. Assay mixed.
- host description · “Peri-rectal swabs were sequenced using a shotgun metagenomic approach”
- host papers[0].abstract · “tracked gastrointestinal resistome and microbiota dynamics of 149 children”
- body site description · “Peri-rectal swabs were sequenced using a shotgun metagenomic approach”
- body site papers[0].abstract · “tracked gastrointestinal resistome and microbiota dynamics of 149 children”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN49165561 | antibiotic_exposure | yes | R4 | 0.50 | paper.abstract | Patients received initial WHO-standard IV therapy |
| SAMN49165601 | collection_date | 2022-01-12 | R1 | 0.85 | biosample.attribute:collection_date | 2022-01-12 |
| SAMN49165561 | country | BE | R1 | 0.90 | sample.attr.geo_loc_name | Belgium: Antwerp |
| SAMN49165601 | health_condition | other_infection | R3 | 0.70 | paper.body.methods | admitted to hospital with severe CAP and judged to require at least 24 h of |
| SAMN49165561 | health_condition | other_disease | R4 | 0.50 | paper.abstract | presenting with severe CAP |
| SAMN49165601 | health_condition_detail | severe community-acquired pneumonia (CAP) | R3 | 0.70 | paper.body.methods | admitted to hospital with severe CAP and judged to require at least 24 h of |
| SAMN49165561 | health_condition_detail | Children hospitalized with severe community-acquired pneumonia (PediCAP trial) | R4 | 0.50 | paper.abstract | presenting with severe CAP |
| SAMN49165601 | latitude | -26.26 | R1 | 0.85 | biosample.attribute:lat_lon | 26.26 S 27.94 E |
| SAMN49165601 | location_locality | Johannesburg | R1 | 0.85 | biosample.attribute:geo_loc_name | South Africa: Johannesburg |
| SAMN49165601 | longitude | 27.94 | R1 | 0.85 | biosample.attribute:lat_lon | 26.26 S 27.94 E |
Sequencing
682 runs over 682 samples · mean 1.54 Gbp per run (median 0.13 Gbp, total 1,050.39 Gbp; 682 runs with a base count) · layout PAIRED 682 · platform ILLUMINA 682 · models NextSeq 500 (682) · 52% of runs with a Sandpiper profile · first public 2026-01-13 – 2026-01-14
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1277853.csv.gz (17.1 KB) · parquet (97.3 KB) — all 682 samples, every field with route and confidence · PRJNA1277853_determinations.csv.gz (32.3 KB) — 5,252 evidence rows