Extragenital testing increases case detection of gonorrhea and chlamydia: The impact of implementing nucleic acid amplification testing
Bibliographic record
Abstract
BACKGROUND: Nucleic acid amplification testing (NAAT) was validated in Ontario in 2018 to test for chlamydia and gonorrhea at extragenital (pharyngeal, rectal) sites. Prior to this validation, extragenital testing could be done only by culture in Ontario. The objective of this study was to determine the number and proportion of gonorrhea and chlamydia cases that were detected exclusively through extragenital (pharyngeal and/or rectal) testing after the implementation of extragenital NAAT for these two infections at Sexual Health Clinic among gay, bisexual, and other men who have sex with men (gbMSM). METHODS: Case and laboratory data from before and after NAAT implementation were used to compare the rates of diagnosis of gonorrhea and chlamydia among gbMSM who presented at Sexual Health Clinics and the percent increase in diagnoses in gbMSM in the entire population. RESULTS: Among gbMSM seen at the clinic after implementation of NAAT testing, 70% of gonorrhea cases and 65% of chlamydia cases were detected exclusively at extragenital sites, corresponding to a four and two-fold increase, respectively, in the average annual number of cases diagnosed. As well, although approximately 50% more pharyngeal than rectal testing occurred, a higher proportion of chlamydia cases were detected rectally than would have been expected; this was not the case for gonorrhea, where most infections were pharyngeal. CONCLUSION: It is important that clinicians perform extragenital testing among gbMSM who have sexual contact involving extragenital sites with more than one partner.
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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 | 0.003 | 0.038 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 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".