Real-time PCR assay design and validation for Prevotella bivia, Peptostreptococcus anaerobius, and Dialister micraerophilus, bacteria associated with increased HIV susceptibility
Bibliographic record
Abstract
Many genital anaerobes, including Prevotella bivia , Peptostreptococcus anaerobius , and Dialister micraerophilus , are underexplored despite being Bacteria Associated with HIV Seroconversion, Inflammation, and immune Cells (BASICs). This is partly due to the lack of molecular tools for their detection and quantification. To address this gap, we designed and validated three real-time qPCR assays for rapid and cost-effective analysis. qPCR assays were designed based on the species-specific core genomes of the three target genital anaerobic species. Assay sensitivity, specificity, and quantification characteristics were assessed using a synthetic oligonucleotide and DNA extracted from closely related species ( n = 27–42) and human urogenital swabs ( n = 111–114). The resultant assays demonstrated 100% sensitivity and specificity for bacterial isolates and high sensitivity (94.6%-97.7%) and specificity (92.8%-95.7%) for human urogenital swabs. The linear dynamic range was 5.0 × 10 1 to 1.0 × 10 7 copies/µL for P. bivia and D. micraerophilus assays, and 2.5 × 10 2 to 1.0 × 10 7 copies/µL for the P. anaerobius assay. Assay efficiency ranged from 99.0% to 112.0%. These assays provide a highly sensitive and specific method for the analysis of bacterial isolates, urogenital samples, and in vitro or ex vivo experiments, which can enhance our understanding of the epidemiology, clinical impact, and biology of key genital anaerobes associated with HIV risk.
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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 | 0.003 | 0.001 |
| 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 | 0.001 | 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".