Pediatric HSCT gut colonization before bloodstream infection
51 fecal/isolate samples from children (<18) undergoing hematopoietic stem cell transplantation, studying gut colonization preceding mucosal barrier injury bloodstream infection; longitudinal design; country not reported. machine-written summary
51 samples · 51 runs · Child · 2019 · 0.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 120 sample values (health condition, health condition detail, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 186 sample values (collection date, health condition, health condition detail, location site) · PMC6861666 |
| – 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 |
longitudinal — not resolved
9 of 9 people sampled more than once (42 samples; median 5, up to 7 per person). Schedule stated by the source: “Weekly fecal samples per patient preceding BSI, plus BCx isolate at BSI onset; day attribute spans from -2 to 29+”.
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 | 51 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 51 | 100% | 9 | 42 | ||
| subject_id | 51 | 100% | 51 | |||
| collection_date | 51 | 100% | 51 | |||
| detailed_location | 51 | 100% | ||||
| health_condition_detail | 51 | 100% | 9 | 42 | ||
| location_site | 51 | 100% | 51 | |||
| timepoint_label | 51 | 100% | 51 |
- Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection in Pediatric Hematopoietic Stem Cell Transplantation Recipients. 2019 PMID 31326608 PMC6861666 own_data
Archive description
Bloodstream infection (BSI) is a frequent complication of hematopoietic stem cell transplantation (HSCT). The gastrointestinal tract is the predicted reservoir for most of these infections. Whole-genome sequencing and comparative genomics can address gaps in our understanding of the dynamics of gut colonization that precede BSI.</p><p>Within a prospective cohort study of children (<18 years) undergoing HSCT, 9 subjects met criteria for mucosal barrier injury BSI. We performed shotgun metagenomics of the blood culture isolate and weekly fecal samples preceding the BSI to compare the genetic similarity of BSI isolates to fecal strains.</p><p>Bacterial strains causing BSIs in pediatric HSCT receipients were observed in the gut microbiota prior to BSI onset, and changes in the abundances of these strains within the gut preceded most BSI episodes. Serial monitoring of the gut microbiota is a promising strategy for identifying HSCT recipients who are high risk for BSI.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of child by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome(51)”
- body site study.description · “weekly fecal samples preceding the BSI”
- life stage study.description · “cohort study of children (<18 years)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11022276 | collection_date | 2015-10/2018-02 | R3 | 0.70 | paper.body.methods_results | at Duke University between October 2015 and February 2018 |
| SAMN11022281 | health_condition | other_infection | R1 | 0.85 | biosample.attribute:isolation_source | isolation_source: BCx |
| SAMN11022276 | health_condition | transplant_or_immunocompromised | R3 | 0.70 | paper.body.methods_results | undergoing evaluation for their first allogeneic or autologous HSCT |
| SAMN11022281 | health_condition_detail | BCx | R1 | 0.85 | biosample.attribute:isolation_source | isolation_source: BCx |
| SAMN11022276 | health_condition_detail | undergoing evaluation for their first allogeneic or autologous HSCT | R3 | 0.70 | paper.body.methods_results | undergoing evaluation for their first allogeneic or autologous HSCT |
| SAMN11022276 | location_site | Duke University | R3 | 0.70 | paper.body.methods_results | undergoing evaluation for their first allogeneic or autologous HSCT at Duke University |
| SAMN11022276 | subject_id | 1 | R1 | 0.85 | sample.attr.patient_id | 1 |
| SAMN11022276 | timepoint_label | -7 | R1 | 0.85 | sample.attr.day | -7 |
Sequencing
51 runs over 51 samples · mean 0.41 Gbp per run (median 0.31 Gbp, total 21.04 Gbp; 51 runs with a base count) · layout PAIRED 51 · platform ILLUMINA 51 · models NextSeq 500 (51) · 67% of runs with a Sandpiper profile · first public 2019-02-27 – 2019-03-05
Authors (0)
No author record.
Downloads
PRJNA524322.csv.gz (2.2 KB) · parquet (71.5 KB) — all 51 samples, every field with route and confidence · PRJNA524322_determinations.csv.gz (2.5 KB) — 306 evidence rows