Comparison of temperate bacteriophages of Pseudomonas aeruginosa from the lungs of chronically infected non-cystic fibrosis bronchiectasis patients over a period 10 years
Bibliographic record
Abstract
The accessory genome of Pseudomonas aeruginosa (PA), is frequently perceived insignificant compared to the core genome, however typically contains temperate bacteriophage (phage) genomes that effect the bacterial host. PA presence in chronically infected lungs correlates with loss of lung function particularly in cystic fibrosis (CF) and non-CF bronchiectasis (nCFBR). This study focuses on isolates from chronically infected nCFBR patients isolated over a decade, shedding light on how temperate phages change over the course of a chronic infection with antibiotic treatment. As temperate phages insert themselves into the bacterial genome they also have the ability to cause genetic diversity to their host’s genome, which drives evolution at an increased rate. By analysing the PA genomes isolated from the chronically infected lungs of patients over a period of 10 years. It was possible to predict the temperate phages in the genomes as well as induce the phages from the bacteria and sequence them. This then identifies which phages are rooted within the genome and which are inducible and therefore may transfer, granting horizontal gene transfer between strains in the lungs. The aim of this study is to ascertain whether by comparing the phages longitudinally and horizontally (when multiple strains were seen within a sample) it is possible to determine if these phage have a role in the PA infection within the lungs becoming chronic. This may also give an idea to why these PA infections are chronic and are so hard to clear from the lung, which is yet unknown.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.011 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".