Molecular typing and genome expression profiling of organ- and host-specific «staphylococcus aureus» from bovine mastitis and human infections
Bibliographic record
Abstract
Staphylococcus aureus has become a major concern in public health and dairy industry due to the rapid evolution of host/organ specialized lineages adapted to humans and major food animals. However, the mechanism(s) of host- and organ-specialization as well as the distribution of dominant clonal lines of S. aureus is presently ill-defined. We hypothesized that coding repeat markers in the intragenic region of clumping factor A (clfA) gene would be capable of detecting and grouping adaptive clones and revealing predominant types and that whole genome expression of these clones in mammary mimicked reduced oxygen condition would potentially reveal subsets of gene(s) responsible for pathways and mechanisms of host-specialization and selection in the mammary gland. Thus, the suitability of clfA was explored. Results indicated that 80% of clfA analyzed had repeat-copies between 44 and 57. Furthermore, human isolates were polymorphic, while mastitis isolates were clonal. The repeats were stable during passages in milk, nutrient broth, and invasion of mammary cells showing suitability for typing. In addition, dominance of a clonal motif in mastitis implied organ-specific selection in the mammary gland. This was further examined in isolates from different organs in human patients and from bovine mastitis. The results showed significant correlation between the organs sampled and the length of clfA. Twenty out of the 23 sputum isolates had lower copy-numbers of 43-48, while 21 out of the 24 skin isolates had 55-63 copies. Moreover, sequence alignments and phylogenetic analysis placed isolates from different hosts and organs into respective clusters.
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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 | 0.000 |
| 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) | 0.000 | 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".