An update on the status of direct testing for <i>Treponema pallidum</i> subspecies <i>pallidum</i> for the laboratory diagnosis of syphilis in Canada
Bibliographic record
Abstract
Background: In Canada, the recent resurgence of infectious syphilis and rising rates of congenital syphilis have renewed interest in direct detection methods for the laboratory diagnosis of syphilis. The Canadian Public Health Laboratory Network (CPHLN) has previously published a series of guidelines for the diagnosis of syphilis in Canada, including the use of direct tests. In the decade since those guidelines were published, laboratory practice has changed. Methods: This systematized review combined a literature search (MEDLINE) of methods for direct detection of Treponema pallidum with an informal survey of current testing practices in Canadian public health laboratories. Results: Direct testing methods have favourable performance characteristics for detection of early syphilis and congenital cases. Although no government licensed commercial nucleic acid amplification test (NAAT) for syphilis is available in Canada, laboratory-developed tests have been implemented in multiple Canadian jurisdictions. Clinical specimens with the highest yield of positive NAAT results for syphilis include genital ulcers, skin lesions, and oral swabs from primary and secondary syphilis patients. For investigation of congenital syphilis, nasopharyngeal, placenta, umbilical cord, blood, and skin lesions are specimens of choice for direct detection of T. pallidum by NAAT. Conclusions: This update on the status of direct testing highlights the importance of NAAT for the detection of T. pallidum, the reduced role of microscopy-based methods, and the emergence of DNA and genome sequencing as tools for phylogenetic analysis and molecular epidemiology.
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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 | 0.010 | 0.034 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.022 | 0.025 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.006 | 0.004 |
| Open science | 0.004 | 0.002 |
| Research integrity | 0.003 | 0.003 |
| Insufficient payload (model declined to judge) | 0.005 | 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".