Inhaled tobramycin effect on CF sputum microbiome
157 sputum samples from people with cystic fibrosis, collected before, during, and after a month-long course of inhaled tobramycin antibiotic therapy, to study treatment effects on the microbiome. machine-written summary
157 samples · 157 runs · US · Age unknown · 2020 · 1.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 305 sample values (subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 628 sample values (antibiotic exposure, country, health condition, health condition detail) · PMC7875198 |
| ○ 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 design single_arm_before_after · population other_disease · Cycled inhaled tobramycin, one-month maintenance course
“cycled, inhaled tobramycin” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
29 of 29 people sampled more than once (150 samples; median 5, up to 7 per person). Schedule stated by the source: “Sputum collected before, weekly during, and after a standard one-month course of inhaled tobramycin; timepoints labeled S0-S5, S32” (time origin: treatment_start).
Genera, mean relative abundance over 145 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 | 0 | 0% | ||||
| country | 157 | 100% | 157 | |||
| health_condition | 157 | 100% | 157 | |||
| subject_id | 150 | 96% | 150 | |||
| antibiotic_exposure | 157 | 100% | 157 | |||
| health_condition_detail | 157 | 100% | 157 | |||
| timepoint_label | 155 | 99% | 155 |
- Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome. 2020 PMID 32631930 PMC7875198 own_data
Archive description
Lung disease in the genetic disease cystic fibrosis (CF) is characterized by chronic, polymicrobial respiratory infections. Antibiotics are a cornerstone of CF lung disease treatment, however, the microbial determinants of response to antibiotics remain poorly understood. The microbiota in CF respiratory specimens are known to be relatively stable over time, even during antibiotic therapy, but less is known about how the metagenome (the predicted functional capacity of the microbiota) changes with antibiotic therapy. The commonly-used antibiotic inhaled tobramycin is known to reduce sputum densities of Pseudomonas aeruginosa and to improve lung disease measures on average in treatment-naïve patients. However, studies have failed to demonstrate a consistent relationship between changes in sputum P. aeruginosa densities and clinical outcomes. We collected CF sputum from 30 individuals with CF before, weekly during and after a standard one-month course of tobramycin, with concomitant lung function measurements and symptom scores collected from all participants. The aim of this study is compare the sputum microbiota and metagenome to clinical outcomes to identify microbial features associated with differential response to tobramycin therapy.
How this project entered the registry
Classified as human lower respiratory / gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.82. Assay shotgun_dna.
- host run.scientific_name · “human lung metagenome”
- body site run.scientific_name · “human lung metagenome”
- body site sample.attr.environment_biome · “human gut (n=157/157)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11310208 | antibiotic_exposure | no | R3 | 0.60 | paper.fulltext.results | no antibiotics other than maintenance azithromycin for ≥1 month |
| SAMN11310208 | country | US | R3 | 0.70 | paper.fulltext.methods | University of Washington Medical Center, Seattle Children |
| SAMN11310208 | health_condition | other_disease | R3 | 0.70 | paper.fulltext.methods | 30 PWCF at three clinical sites |
| SAMN11310208 | health_condition_detail | Cystic fibrosis (PWCF) with chronic P. aeruginosa lung infection | R3 | 0.60 | paper.fulltext.methods | 30 PWCF at three clinical sites |
| SAMN11310208 | subject_id | N101 | R1 | 0.70 | sample.name_rule:library_names | N101S0 |
| SAMN11310208 | timepoint_label | S0 | R1 | 0.70 | sample.name_rule:library_names | N101S0 |
Sequencing
157 runs over 157 samples · mean 1.11 Gbp per run (median 1.01 Gbp, total 173.51 Gbp; 157 runs with a base count) · layout PAIRED 157 · platform ILLUMINA 157 · models Illumina HiSeq 2500 (157) · 92% of runs with a Sandpiper profile · first public 2020-04-14
Authors (19)
Nelson MT first · Wolter DJ · Eng A · Weiss EJ · Vo AT · Brittnacher MJ · Hayden HS · Ravishankar S · Bautista G · Ratjen A · Blackledge M · McNamara S · Nay L · Majors C · Miller SI · Borenstein E · Simon RH · LiPuma JJ · Hoffman LR last
Downloads
PRJNA530252.csv.gz (4.5 KB) · parquet (75.1 KB) — all 157 samples, every field with route and confidence · PRJNA530252_determinations.csv.gz (6.5 KB) — 933 evidence rows