Isolation and characterisation of bacteriophages infecting environmental strains of Clostridium difficile
Bibliographic record
Abstract
Clostridium difficile is a leading cause of nosocomial infections associated with antibiotic treatment. Despite its’ pathogenic role, the bacterium can be carried asymptomatically in the GI tract and has an ubiquitous presence in the environment. The ecology of C. difficile outside clinical settings is not fully understood, but the evolution of pathogenic strains may occur in its zoonotic and environmental reservoirs. A major driver of bacterial genome evolution is bacteriophages. This project has investigated the prevalence and diversity of phages associated with strains from these reservoirs. A large and diverse collection of C. difficile isolates was established in order to isolate and characterise the phages associated with them. \n27 phages were isolated. These were characterised according to their particle morphology, genome size and plaque morphology which showed they could be sub-grouped according to morphology. Host range analyses showed there is a complex network of phage-host interactions within this species. \nTo characterise to a genetic level, the genomes of seven phages were sequenced and annotated. Their genomes show they are related to known C. difficile phages. However, genes which are unusual or novel to phage genomes were also identified. \nComparative genomics identified distinct lineages within C. difficile phages, which correspond to their morphological sub-grouping. Also the bioinformatic analyses provide evidence of genetic exchange occurring between them, presumably during co-infection as multiple prophage carriage is common in this species. Interestingly, analysis of the C. difficile CRISPR system showed that in addition to the bacterial arrays, several prophages encode CRISPR arrays that target phage sequences. Evidence of their co-evolution suggests phage infection impacts both genome evolution of their host and other C. difficile phages. \nIn summary, a diverse C. difficile phage collection has been established which has the potential for development to allow their exploitation.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.062 | 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".