Molecular epidemiological characteristics of <i>Mycobacterium abscessus</i> complex in non-cystic fibrosis patients in Japan and Taiwan
Bibliographic record
Abstract
Abstract Mycobacterium abscessus complex (MABC) is an emerging non-tuberculous mycobacterium (NTM). Specific MABC clones are reportedly spreading globally in cystic fibrosis (CF) patients, however, associated genomic epidemiology studies are lacking in East Asia. Analysis of whole-genome sequencing data for MABC isolates from 220 pre-treatment, non-CF patients in Japan and Taiwan revealed that 112/220, 105/220, and 3/220 were M. abscessus subsp. abscessus (ABS), M. abscessus subsp. massiliense (MAS), and M. abscessus subsp. bolletii (BOL), respectively. No significant differences in subspecies composition were noted based on location. Moreover, >50% of ABS and >70% of MAS were related to four predominant clones in the region. Known mutations conferring acquired macrolide resistance were rare (1.4%) and not enriched in the predominant clones. Conversely, the macrolide-susceptible erm (41) T28C mutation was significantly enriched in one predominant ABS clone. The most predominant ABS clone was genetically related to the dominant circulating clone (DCC). Hence, we have clarified the relationship between the predominant clones in Japan and Taiwan, and those reported in the international CF patient community. Our results provide insights regarding the genetic characteristics of globally dominant and area-specific strains isolated from patients with or without CF, as well as differences between globally spread and regionally-specific 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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 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".