Infant stool metagenomics for Campylobacter species in Peru
Case series of 83 stool samples from children under 2 years old in Loreto, Peru, with diarrheal disease or asymptomatic carriage, qPCR-positive for Campylobacter but negative for C. jejuni/C. coli, analyzed by shotgun metagenomic sequencing to identify the causative species. machine-written summary
83 samples · 39 runs · PE · Infant / toddler · 2023 · 0.21 Gbp / sample · cohort Peru Loreto LMIC infant stool cohort
One study deposited as 2 BioProjects (97 catalog samples together): PRJNA834762 · PRJNA837236 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 210 sample values (collection date, country, sex) |
| ✓ Abstract / description | 83 sample values (location locality) |
| – 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 26 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 | 0 | 0% | ||||
| country | 83 | 100% | 83 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 83 | 100% | 83 | |||
| detailed_location | 83 | 100% | ||||
| location_locality | 83 | 100% | 83 | |||
| sex | 44 | 53% | 44 |
- (no title) curated
- (no title) curated
- (no title) curated
Archive description
Campylobacter sp. are a major cause of bacterial diarrhea worldwide and are associated with high rates of mortality and linear growth faltering in children living in low- to middle-income countries (LMICs). Campylobacter jejuni and C. coli are most often the causative agents of enteric disease among children in LMICs. However, there are many stool samples from children under 2 years of age with acute diarrheal disease or asymptomatic carriers living in a low resource community in Peru that are qPCR positive for Campylobacter species but qPCR negative for C. jejuni and C. coli. The goal of this study was to determine if whole-genome shotgun metagenomic sequencing (WSMS) could identify the Campylobacter species within these samples.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “infant stool whole-genome shotgun metagenomic”
- life stage study.description · “children under 2 years of age”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN28455912 | collection_date | 2010-11-10 | R1 | 0.85 | biosample.attribute:collection_date | 2010-11-10 |
| SAMN28455912 | country | PE | R1 | 0.90 | biosample_attr | Peru:Loreto |
| SAMN28455912 | location_locality | Iquitos | R4 | 0.50 | paper.abstract | children living in Iquitos, Peru |
| SAMN28455912 | sex | male | R1 | 0.90 | biosample_attr | Male |
Sequencing
83 runs over 83 samples · mean 0.24 Gbp per run (median 0.21 Gbp, total 19.91 Gbp; 83 runs with a base count) · layout PAIRED 83 · platform ILLUMINA 83 · models Illumina MiSeq (83) · 31% of runs with a Sandpiper profile · first public 2022-05-19 – 2023-12-10
Authors (16)
Parker CT first · Schiaffino F · Huynh S · Paredes Olortegui M · Peñataro Yori P · Garcia Bardales PF · Pinedo Vasquez T · Curico Huansi GE · Manzanares Villanueva K · Shapiama Lopez WV · Cooper KK · Kosek MN last · Mourkas E · Pascoe B · Houpt ER · Liu J
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA834762.csv.gz (3.1 KB) · parquet (73.2 KB) — all 83 samples, every field with route and confidence · PRJNA834762_determinations.csv.gz (2.2 KB) — 293 evidence rows