Blood isolate genomes from critically ill adults
246 samples from critically ill adult patients in Philadelphia, PA, comprising whole genome sequences of bloodstream infection isolates studied alongside gut microbiomes in a longitudinal design. machine-written summary
246 samples · 246 runs · US · Age unknown · 2023 · 1.81 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,722 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 738 sample values (health condition, health condition detail, location site) · PMC10564172 |
| ○ 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
design observational_with_procedure
longitudinal
54 of 136 people sampled more than once (164 samples; median 2, up to 7 per person) · follow-up median 8 d (max 2 mo) · median interval between samples 4 d (time from collection dates).
Each row is one person (36 shown of 54); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 208 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 | 246 | 100% | ||||
| country | 246 | 100% | 246 | |||
| health_condition | 246 | 100% | 246 | |||
| subject_id | 246 | 100% | 246 | |||
| collection_date | 246 | 100% | 246 | |||
| detailed_location | 246 | 100% | ||||
| health_condition_detail | 246 | 100% | 246 | |||
| latitude | 246 | 100% | 246 | |||
| location_locality | 246 | 100% | 246 | |||
| location_region | 246 | 100% | 246 | |||
| location_site | 246 | 100% | 246 | |||
| longitude | 246 | 100% | 246 |
- Tracking gut microbiome and bloodstream infection in critically ill adults. 2023 PMID 37816004 PMC10564172 own_data
Archive description
Our study investigated whether BSI organisms were associated with gut microbiome presence. The genomes presented were the blood culture isolates for the patients we enrolled in our study and sequenced as a reference for our gut microbiome analysis.
How this project entered the registry
Classified as human blood / tissue / internal fluids / gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “WGS blood culture isolates from critically ill patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN29636406 | collection_date | 2021-01-08 | R1 | 0.90 | biosample.attribute:collection_date | 2021-01-08 |
| SAMN29636406 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Philadelphia, PA |
| SAMN29636406 | health_condition | other_disease | R3 | 0.70 | paper.fulltext.methods | Patients admitted to the medical ICU |
| SAMN29636406 | health_condition_detail | critically ill patients admitted to medical ICU | R3 | 0.70 | paper.fulltext.methods | Patients admitted to the medical ICU |
| SAMN29636406 | latitude | 39.9500 | R1 | 0.90 | biosample.attribute:lat_lon | 39.95 N 75.19 W |
| SAMN29636406 | location_locality | Philadelphia | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Philadelphia, PA |
| SAMN29636406 | location_region | Pennsylvania | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Philadelphia, PA |
| SAMN29636406 | location_site | Hospital of the University of Pennsylvania | R3 | 0.70 | paper.fulltext.methods | medical ICU of the Hospital of the University of Pennsylvania |
| SAMN29636406 | longitude | -75.1900 | R1 | 0.90 | biosample.attribute:lat_lon | 39.95 N 75.19 W |
| SAMN29636406 | subject_id | S088 | R1 | 0.85 | sample.attr.host_subject_id | S088 |
Sequencing
246 runs over 246 samples · mean 2.27 Gbp per run (median 1.81 Gbp, total 559.64 Gbp; 246 runs with a base count) · layout PAIRED 246 · platform ILLUMINA 246 · models Illumina NovaSeq 6000 (180), Illumina HiSeq 2500 (66) · 87% of runs with a Sandpiper profile · first public 2023-08-27
Authors (11)
Gu CH first · Khatib LA · Fitzgerald AS · Graham-Wooten J · Ittner CA · Sherrill-Mix S · Chuang Y · Glaser LJ · Meyer NJ · Bushman FD · Collman RG last
Downloads
PRJNA848838.csv.gz (8.2 KB) · parquet (81.8 KB) — all 246 samples, every field with route and confidence · PRJNA848838_determinations.csv.gz (16.4 KB) — 2,460 evidence rows