Trends in the molecular epidemiology and population genetics of emerging<i>Sporothrix</i>species
Bibliographic record
Abstract
Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation ofParacoccidioidespropagules from the environment. The main agents include members of theP. brasiliensiscomplex (phylogenetically-defined species S1, PS2, PS3, and PS4) andP. lutzii. DNA-sequencing of protein-coding loci (e.g.,GP43,ARF, andTUB1) is the reference method for recognizingParacoccidioidesspecies due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity withinParacoccidioides. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotypingParacoccidioidesspecies. The bioinformatic analysis generated 144in silicoAFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC/MseI-CT and #2 EcoRI-AT/MseI-CT). The combinations #1 and #2 were usedin vitroto genotype 165Paracoccidioidesisolates recovered from across a vast area of South America. Considering the overall scored AFLP markersin vitro(67-87 fragments), the values of polymorphism information content (PIC= 0.3345-0.3456), marker index (MI= 0.0018), effective multiplex ratio (E= 44.6788-60.3818), resolving power (Rp= 22.3152-34.3152), discriminating power (D= 0.5183-0.5553), expected heterozygosity (H= 0.4247-0.4443), and mean heterozygosity (Havp = 0.00002-0.00004), demonstrated the utility of AFLP markers to speciateParacoccidioidesand to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability amongP. brasiliensiscomplex andP. lutzii(PhiPT = 0.651-0.658,P < 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions ofMAT1-1orMAT1-2idiomorphs were not significantly skewed (1:1 ratio) forP. brasiliensis s. str.(χ2= 1.025;P= 0.3113),P. venezuelensis(χ2= 0.692;P= 0.4054), andP. lutzii(χ2= 0.027;P= 0.8694), supporting random mating within each species. In contrast, skewed distributions were found forP. americana(χ2= 8.909;P= 0.0028) andP. restrepiensis(χ2= 4.571;P= 0.0325) with a preponderance ofMAT1-1. Geographical distributions confirmed thatP. americana,P. restrepiensis, andP. lutziiare more widespread than previously thought.P. brasiliensis s. str.is by far the most widely occurring lineage in Latin America countries, occurring in all regions of Brazil. Our new DNA fingerprint assay proved to be rapid, reproducible, and highly discriminatory, to give insights into the taxonomy, ecology, and epidemiology ofParacoccidioidesspecies, guiding disease-control strategies to mitigate PCM.
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 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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| 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".