Respiratory/GI microbiome in LTACH patients, Philadelphia
567 respiratory and gastrointestinal tract samples from long-term acute care hospital residents in Philadelphia, PA, in a cross-sectional study of microbiome/resistome change under antibiotic pressure. machine-written summary
567 samples · 567 runs · US · Adult · 2019 · 6.1 Mbp / sample
One study deposited as 2 BioProjects (902 catalog samples together): PRJNA545794 · PRJNA546227 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,969 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ✓ Abstract / description | 567 sample values (antibiotic exposure) |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
hospital ward — not resolved
Residents of long-term acute care hospital(s) (LTACH); number of facilities / units not stated; no sub-unit ids.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 567 | 100% | ||||
| country | 567 | 100% | 567 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 567 | 100% | 567 | |||
| antibiotic_exposure | 567 | 100% | 567 | |||
| collection_date | 567 | 100% | 567 | |||
| detailed_location | 567 | 100% | ||||
| latitude | 567 | 100% | 567 | |||
| location_locality | 567 | 100% | 567 | |||
| location_region | 567 | 100% | 567 | |||
| longitude | 567 | 100% | 567 |
Archive description
We applied metagenomic sequencing to respiratory and gastrointestinal tract specimens, collected from a cohort of long-term acute care hospital (LTACH) residents, in order to define microbiome and resistome change under antibiotic pressure, generate microbiome disruption indices (MDIs) to predict risk for multidrug-resistant infection, and contribute to a deeper understanding of how antibiotics and other medications increase risk of specific AMR gene selection and persistence.
How this project entered the registry
Classified as human lower respiratory / gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Respiratory Tract Microbial Community Change”
- body site study.description · “respiratory and gastrointestinal tract specimens”
- life stage study.description · “long-term acute care hospital (LTACH) residents”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11930451 | antibiotic_exposure | yes | R4 | 0.50 | study.description | microbiome and resistome change under antibiotic pressure |
| SAMN11930451 | collection_date | 2017-05-05 | R1 | 0.90 | biosample.attribute:collection_date | 2017-05-05T00:00:00Z |
| SAMN11930451 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Philadelphia, PA |
| SAMN11930451 | latitude | 39.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 39.57 N 75.11 W |
| SAMN11930451 | location_locality | Philadelphia | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Philadelphia, PA |
| SAMN11930451 | location_region | Pennsylvania | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Philadelphia, PA |
| SAMN11930451 | longitude | -75.1100 | R1 | 0.90 | biosample.attribute:lat_lon | 39.57 N 75.11 W |
| SAMN11930451 | subject_id | MIRA_022 | R1 | 0.85 | sample.attr.subject_id | MIRA_022 |
Sequencing
567 runs over 567 samples · mean 19.2 Mbp per run (median 6.1 Mbp, total 10.91 Gbp; 567 runs with a base count) · layout PAIRED 567 · platform ILLUMINA 567 · models Illumina HiSeq 2500 (567) · 3% of runs with a Sandpiper profile · first public 2019-06-02
Authors (0)
No author record.
Downloads
PRJNA545794.csv.gz (12.5 KB) · parquet (88.5 KB) — all 567 samples, every field with route and confidence · PRJNA545794_determinations.csv.gz (29.1 KB) — 4,536 evidence rows