The role of gene copy number variation in antimicrobial resistance in human fungal pathogens
Bibliographic record
Abstract
Faced with the burden of increasing resistance to antifungals in many fungal pathogens and the constant emergence of new drug-resistant strains, it is essential to assess the importance of various resistance mechanisms. Fungi have relatively plastic genomes and can tolerate genomic copy number variation (CNV) caused by aneuploidy and gene amplification or deletion. In many cases, these genomic changes lead to adaptation to stressful conditions, including those caused by antifungal drugs. Here, we specifically examine the contribution of CNVs to antifungal resistance. We undertook a thorough literature search, collecting reports of antifungal resistance caused by a CNV, and classifying the examples of CNV-conferred resistance into four main mechanisms. We find that in human fungal pathogens, there is little evidence that gene copy number plays a major role in the emergence of antifungal resistance compared to other types of mutations. We discuss why we might be underestimating their importance and new approaches being used to study them.
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".