Organ- and Host-Specific Clonal Groups of <i>Staphylococcus aureus</i> from Human Infections and Bovine Mastitis Revealed by the Clumping Factor A Gene
Bibliographic record
Abstract
Staphylococcus aureus has become a major concern in public health because of the rapid evolution of resistant and host/organ specialized lineages adapted to humans and major food animals. However, the mechanism(s) of host and organ specializations in S. aureus is presently ill defined. The objective of our study was to investigate whether coding intragenic repeat-containing markers would be capable of detecting and grouping adaptive clones, tracing their sources, or studying the basis for their specializations in different microenvironments. We have analyzed the number of copies as well as the nucleotide sequences in the hypervariable R-domain of the clumping factor A gene in 95 isolates from different organs in human patients and from bovine mastitis, using polymerase chain reaction, sequencing, multiple sequence alignment, and phylogenetic relationships. The results showed that isolates of the same human organ were polymorphic for clfA, whereas those of the mammary were clonal. Twenty of the 23 sputum isolates had lower copy numbers of 43-48, while 21 of the 24 skin isolates had 55-63 copies. Twenty-four repeat types were identified with the index of discrimination of 0.9. Repeat types and overall sequence pattern groups were highly consistent. In addition, sequence alignments and phylogenetic analysis placed the isolates from different hosts and organs into respective clusters. Thus, clfA is useful in detecting the clonal lineage of mastitis, and tracing and grouping organ-specific strains, and might be a potential tool for studying host specialization and selection.
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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 | 0.001 |
| 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".