Bibliographic record
Abstract
The non-aureus staphylococci (NAS) species are among the most prevalent isolated from bovine milk and have been reported to inhibit major mastitis pathogens, likely by producing bacteriocins. This thesis is comprised of two sections, focusing on in vitro inhibition assays and in silico identification of bacteriocin gene clusters and bacteriocin resistance genes in NAS and Staphylococcus aureus, using isolates obtained from the Canadian Bovine Mastitis and Milk Quality Research Network. The first part determined the inhibitory capability of 441 bovine NAS isolates (comprising 25 species) against bovine S. aureus and human methicillin-resistant S. aureus (MRSA) and determined the presence of bacteriocin biosynthetic gene clusters in NAS whole genomes. Overall, 40 isolates from 9 species (S. capitis, S. chromogenes, S. epidermidis, S. pasteuri, S. saprophyticus, S. sciuri, S. simulans, S. warneri, and S. xylosus) inhibited growth of S. aureus in vitro; of which, 23 isolates (from S. capitis, S. chromogenes, S. epidermidis, S. pasteuri, S. simulans, and S. xylosus) also inhibited MRSA. 105 putative bacteriocin gene clusters encompassing 6 different subclasses (lanthipeptides, sactipeptides, lasso peptides, class IIa, class IIc, and class IId) in 95 whole genomes from 16 species were identified. The second part of the thesis determined the susceptibility of 139 bovine S. aureus isolates to a bacteriocin producing S. chromogenes isolate and identified and described the distribution of genes potentially associated with susceptibility and resistance in S. aureus whole genomes. Overall, 90 S. aureus isolates (65%) were resistant to inhibition by the S. chromogenes isolate. We identified 77 genes that were associated with an isolate being resistant. We also identified 76 genes that were associated with an isolate being susceptible to the S. chromogenes. Bacteriocin susceptibility and resistance seems to be linked to a large number of genes, the majority of which are annotated as hypothetical proteins and will need further assessment to determine their role in S. aureus susceptibility. Overall, bacteriocins may be a potential source of novel antimicrobials and this thesis represents the foundation to explore novel NAS bacteriocins.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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 source (direct Gemma or distilled Codex), 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".