Microbiome in Salmonella Typhi susceptibility
96 fecal samples from volunteers challenged with S. Typhi or S. Paratyphi A, collected over 90 days post-infection. Study examines microbiome composition associated with typhoid fever development and antibiotic treatment. machine-written summary
96 samples · 96 runs · GB · Adult · 2019 · 2.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 96 sample values (subject id) |
| ✓ Abstract / description | 192 sample values (antibiotic exposure, health condition) |
| ✓ Full text | 96 sample values (country) · PMC12281769 |
| ○ 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 Other administered intervention (see intervention_detail) design single_arm_before_after · population gi_infection_or_diarrhoea · Human challenge with S. Typhi/Paratyphi A, then antibiotic treatment
“volunteers are challenged with 10(4) S. Typhi” — bioproject.description (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 85 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 |
- Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model. 2025 PMID 40696437 PMC12281769 own_data
- Interplay Between the Gut Microbiome and Typhoid Fever: Insights from Endemic Countries and a Controlled Human Infection Model 2024 own_data
Archive description
This study addresses the role of the intestinal microbiome in susceptibilty to Salmonella Typhi and Salmonella Paratyphi A in a human challenge model. Briefly, volunteers are challenged with 10(4) S. Typhi or 10(3) S. Paratyphi Ai and monitored over a two-week period for clinical signs of typhoid fever. Approximately sixty percent of challenged volunteers develop typhoid fever. All volunteers receive antibiotic treatment. The study takes fecal samples from challenged individuals and studies microbiome composition day 0, 7, 14, 28 and 90 post challenge. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.description · “volunteers are challenged with 10(4) S. Typhi”
- body site study.description · “The study takes fecal samples”
- life stage study.description · “volunteers are challenged with 10(4)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104500557 | antibiotic_exposure | yes | R4 | 0.50 | study.description | All volunteers receive antibiotic treatment |
| SAMEA104500557 | country | GB | R3 | 0.70 | paper.fulltext.abstract | a UK population |
| SAMEA104500557 | health_condition | gi_infection_or_diarrhoea | R4 | 0.30 | study.description | volunteers are challenged with 10(4) S. Typhi or 10(3) S. Paratyphi |
| SAMEA104500557 | subject_id | PATCH7278458 | R1 | 0.85 | sample.attr.subject_id | PATCH7278458 |
Sequencing
96 runs over 96 samples · mean 2.16 Gbp per run (median 2.18 Gbp, total 206.94 Gbp; 96 runs with a base count) · layout PAIRED 96 · platform ILLUMINA 96 · models Illumina HiSeq 2500 (96) · 89% of runs with a Sandpiper profile · first public 2019-03-12
Authors (35)
Ashton PM first · Mageiros L · Meiring JE · Chunga-Chirambo A · Khanam F · Dongol S · Banda H · Karkey A · Preciado-Llanes L · Thomaides-Brears H · Gibani M · Rajib NH · Rahman N · Biswas PK · Bhuiyan MAI · Kay S · Auger K · Seret O · Thomson NR · Pollard AJ · Baker S · Basnyat B · Clemens JD · Dolecek C · Dunstan SJ · Dougan G · Heyderman RS · Pitzer VE · Qadri F · Gordon MA · Holt KE · Darton TC · STRATAA Study Group last · Chirambo AC · Llanes LP
Downloads
PRJEB22175.csv.gz (3.1 KB) · parquet (73.3 KB) — all 96 samples, every field with route and confidence · PRJEB22175_determinations.csv.gz (3.2 KB) — 384 evidence rows