Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution
Bibliographic record
Abstract
(MAH) is a clinically important species of non-tuberculous mycobacteria that causes infections in a variety of hosts. This opportunistic pathogen is widespread in the environment, including natural and engineered water systems across the globe. To examine the current genetic diversity of this organism, we analysed 702 MAH genomes isolated from humans, pigs and environmental sources across six countries and three continents. Through Bayesian population structure analysis, we identified ten distinct global lineages, including seven previously described and three new ones. Several lineages exhibited regional clustering, including sequence cluster 6 (SC6) in Germany and SC8 in both the USA and Germany. Further analysis identified recombination hotspots in membrane proteins associated with virulence, antimicrobial resistance and immune modulation, driven by insertion sequences and other elements that frequently integrate at tRNA gene sites. This work demonstrates the remarkable genomic diversity of MAH and provides insight into the evolutionary mechanisms that contribute to its success as a pathogen in both humans and animals.
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) | 0.000 | 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 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".