Gut/respiratory microbiome in LTACH patients, Philadelphia
Metagenomic Study of Gastrointestinal Tract Microbial Community Change During Long-Term Acute Care
335 samples from long-term acute care hospital residents in Philadelphia, PA, profiling gastrointestinal and respiratory microbiome and resistome changes under antibiotic pressure in a longitudinal design. machine-written summary
335 samples · 335 runs · US · Age unknown · 2019 · 2.01 Gbp / sample
One study deposited as 2 BioProjects (902 catalog samples together): PRJNA545794 · PRJNA546227 · show together
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinal
34 of 42 people sampled more than once (327 samples; median 6, up to 65 per person) · follow-up median 32 d (max 12 mo) · median interval between samples 4 d(time from collection dates).
Schedule stated by the source: “Repeated stool swab sampling per subject over time during LTACH stay; median 5, max 65 samples per subject across 42 subjects.”.
Each row is one person (34 shown); dots are samples at days since that person's first sample.
Bacteroides 20.0%Pseudomonas 6.8%Klebsiella 6.1%Alistipes 5.3%Parabacteroides 4.5%Phocaeicola 3.6%Enterococcus 2.9%Enterocloster 2.8%Enterococcus_B 2.6%Ruthenibacterium 2.3%Akkermansia 2.2%Escherichia 1.7%not assigned to a genus 6.2%other genera 33.0%
Genera, mean relative abundance over 301 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
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 gut / stool / lower respiratory shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
hostrun.host_tax_id · “9606”
hoststudy.description · “long-term acute care hospital (LTACH) residents”
body sitestudy.description · “respiratory and gastrointestinal tract specimens”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN11954206
collection_date
2017-07-07
R1
0.90
biosample.attribute:collection_date
2017-07-07T00:00:00Z
SAMN11954206
country
US
R1
0.90
sample.attr.geo_loc_name
USA: Philadelphia, PA
SAMN11954206
latitude
39.5700
R1
0.90
biosample.attribute:lat_lon
39.57 N 75.11 W
SAMN11954206
lifestyle
institutionalized
R4
0.45
ena.study_description
long-term acute care hospital (LTACH) residents
SAMN11954206
lifestyle_detail
long-term acute care hospital (LTACH) residents
R4
0.45
ena.study_description
long-term acute care hospital (LTACH) residents
SAMN11954206
location_locality
Philadelphia
R1
0.85
biosample.attribute:geo_loc_name
USA: Philadelphia, PA
SAMN11954206
location_region
Pennsylvania
R1
0.75
biosample.attribute:geo_loc_name
USA: Philadelphia, PA
SAMN11954206
longitude
-75.1100
R1
0.90
biosample.attribute:lat_lon
39.57 N 75.11 W
SAMN11954206
subject_id
MIRA_030
R1
0.85
sample.attr.subject_id
MIRA_030
Sequencing
335 runs over 335 samples · mean 1.97 Gbp per run (median 2.01 Gbp, total 659.39 Gbp; 335 runs with a base count) · layout PAIRED 335 · platform ILLUMINA 335 · models Illumina HiSeq 2500 (335) · 90% of runs with a Sandpiper profile · first public 2019-06-05
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata