Addressing a dual public health emergency: supporting physicians to prescribe opioid medications
Bibliographic record
Abstract
<h3>Aims</h3> Carbapenem resistance in <i>Bacteroides fragilis</i> is emerging and is mainly attributed to insertion sequence (IS)-mediated activation of the carbapenemase gene <i>cfiA</i>. We investigated the use of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and the CarbaNP assay for the rapid identification of these strains. <h3>Methods</h3> This study used the Bruker MALDI Biotype system and the mass spectra models generated by 20 <i>B. fragilis</i> reference strains (10 <i>cfiA</i>-positive and 10 <i>cfiA</i>-negative) in the ClinProTools software to identify 404 <i>B. fragilis</i> (71 <i>cfiA</i>-positive and 333 <i>cfiA</i>-negative) clinical isolates. The ability of the CarbaNP assay to detect IS-mediated activation of the <i>cfiA</i> gene was assessed and the results obtained by molecular analysis were used as reference methods. <h3>Results</h3> The support vector machine model generated by ClinProTools was found to be the most reliable algorithm for differentiation of <i>cfiA</i>-positive and <i>cfiA</i>-negative <i>B. fragilis</i> subgroups. Using the direct transfer method, all but one <i>cfiA</i>-negative isolates were correctly identified to the two subgroups by the model. The correct identification of the <i>cfiA</i>-negative isolate was obtained upon retesting by the extraction method. Of the 81 <i>cfiA</i>-positive isolates, PCR and sequencing showed that 30 had an IS element providing the promoter for activation of <i>cfiA</i>. With regard to the presence of the IS element, the CarbaNP test in the <i>cfiA</i> upstream region had 100% sensitivity, 80.4% specificity, 75.0% positive predictive value and 100% negative predictive value. <h3>Conclusions</h3> The combination of MALDI-TOF MS and the CarbaNP assay can be applied in diagnostic clinical laboratory for rapid identification of <i>B. fragilis</i> with IS element-activated <i>cfiA</i> gene.
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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 | 0.002 | 0.007 |
| 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) | 0.002 | 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".