Comparison of Three Assays for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in SurePath Pap Samples and the Role of Pre- and Postcytology Testing
Bibliographic record
Abstract
Chlamydia trachomatis and Neisseria gonorrhoeae are common causes of sexually transmitted infections, and there is interest in screening SurePath liquid-based Pap (L-Pap) samples with Aptima Combo 2 (AC2), Amplicor (AMP), and ProbeTec ET (PT) assays. SurePath L-Pap samples and a cervical swab (CS) were collected from 394 women attending health clinics in Hamilton and Toronto, ON, Canada. L-Pap samples were tested with the three assays prior to being processed for cytology, and the CS sample was tested with AC2. The prevalence of C. trachomatis was 8.9%, and that of N. gonorrhoeae was 1.5%. By using the positives from CS testing, as well as CS negatives corresponding to L-Pap samples that tested positive in 2 of 3 assays, the sensitivities of AC2, AMP, and PT for C. trachomatis in precytology samples were calculated to be 97.1% (34 of 35 positive samples were detected), 91.4% (32 of 35 were detected), and 77.1% (27 of 35 were detected), respectively. Six women were infected with N. gonorrhoeae. After cytology processing, the results of testing the remaining liquid in the L-Pap vial and the cell-enriched fraction for C. trachomatis by AC2 showed positive agreements of 98.9% (kappa [k], 0.93) and 98.7% (k, 0.92), respectively, with the results of testing precytology L-Pap samples. Although all testing showed high specificity, testing for C. trachomatis by AC2 was significantly more sensitive than testing by PT for SurePath samples (P = 0.02). Newer versions of AMP (Cobas 4800) and PT (Q(x) with XTR technology) need published evaluations for detecting C. trachomatis and N. gonorrhoeae in L-Pap samples. C. trachomatis testing can be performed with similar results on pre- and postcytology SurePath samples.
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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 | 0.009 | 0.017 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".