Bibliographic record
Abstract
Shigella spp. are pathogens responsible for the global burden of diarrhoeal disease. The genus is comprised of four species: Shigella sonnei, Shigella boydii, Shigella flexneri and Shigella dysenteriae, each phylogenetically different but phenotypically and pathogenically similar. Previous work by the McPhee lab examining the two-component signalling cascade PhoPQ-PmrD-PmrAB identified a mutation in pmrD which resulted in the loss of PmrD protein in S. flexneri M90T. Here, I investigate whether there is a loss of PmrD-PmrAB signalling cascade in other strains of Shigella besides S. flexneri M90T. Using pangenome analysis we construct a core-gene phylogeny and find our results in agreement with previous findings that Shigella spp has multiple origins of evolution. In our work we also show their genomes spread over five prominent clusters, interspersed within Escherichia genomes. Further, we look for genomic variations of pmrD and pmrA, and identified a total of 11 distinct variations; 4 of pmrD and 7 of pmrA. Using in vitro microbiology techniques, we found that one variation, a truncated pmrA present in a subset of S. dysenteriae strains did not maintain PmrAB-regulated polymyxin B resistance. We also show that the PmrD-PmrAPmrB signalling cascade does not modulate O antigen length in a dominate variant of pmrD present in all S. flexneri strains or the truncated pmrA present in some S. dysenteriae strains.
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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) | 0.001 | 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".