Metagenomic confirmation of Shigella in diarrheal cases
27 fecal samples from diarrheal cases in Kolkata (India), Bamako (Mali), and Manhica (Mozambique), used to validate qPCR-based Shigella detection via metagenomics; case series/case-control design. machine-written summary
27 samples · 27 runs · IN, ML, MZ · Infant / toddler · 2017 · 29.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 54 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12211052, PMC5786726 |
| ✓ Supplementary tables | 27 sample values (subject id) |
| ✓ External resources | 54 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 27 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 | 27 | 100% | 27 | |||
| health_condition | 27 | 100% | 27 | |||
| subject_id | 27 | 100% | 27 | |||
| collection_date | 27 | 100% | 27 | |||
| health_condition_detail | 27 | 100% | 27 |
- Fecal microbiome profiling of children with Shigella diarrhea from low- and middle-income countries. 2025 PMID 40497681 PMC12211052 cites_accession
- Direct Detection of Shigella in Stool Specimens by Use of a Metagenomic Approach. 2018 PMID 29118177 PMC5786726 own_data
Archive description
The importance of Shigella species as a cause of childhood diarrhea disease has become increasingly apparent with quantitative (q)PCR based diagnostic methods versus culture. We sought to validate qPCR-based detection of Shigella via a metagenomics approach using 27 fecal samples isolated from three countries of the Global Enteric Multicenter Study.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “approach using 27 fecal samples isolated from”
- 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 · “a cause of childhood diarrhea disease has”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07357503 | collection_date | 2009-03-27 | R1 | 0.85 | biosample.attribute:collection_date | 2009-03-27 |
| SAMN07357503 | country | ML | R1 | 0.90 | biosample_attr | Mali: Bamako |
| SAMN07357503 | health_condition | gi_infection_or_diarrhoea | R2 | 0.75 | external.gmrepo source | phenotype: Diarrhea |
| SAMN07357503 | health_condition_detail | Diarrhea | R2 | 0.75 | external.gmrepo source | phenotype: Diarrhea |
| SAMN07357503 | subject_id | 202260 | R2 | 0.85 | paper.supp.JCM.01374-17_zjm999095800s1.pdf[page1_txt!ID] | 202260 |
Sequencing
27 runs over 27 samples · mean 29.42 Gbp per run (median 29.39 Gbp, total 794.32 Gbp; 27 runs with a base count) · layout PAIRED 27 · platform ILLUMINA 27 · models Illumina HiSeq 4000 (27) · 100% of runs with a Sandpiper profile · first public 2017-12-10
Authors (0)
No author record.
Downloads
PRJNA394687.csv.gz (1.9 KB) · parquet (70.7 KB) — all 27 samples, every field with route and confidence · PRJNA394687_determinations.csv.gz (2.2 KB) — 135 evidence rows