P2.030 Utility of<i>Neisseria Gonorrhoea</i>Positive APTIMA Specimens to Assess Strain Diversity and Antibiotic Resistance
Bibliographic record
Abstract
Background Samples collected from community patients and patients visiting the Sexually Transmitted Infection (STI) clinics, submitted for the detection of Neisseria gonorrhoea (NG) in Alberta, Canada, are tested by the FDA approved APTIMA Combo 2® assay (GEN-PROBE). In addition swabs are collected from a limited number of high risk patients for culture and susceptibility testing. The isolates can also be used for molecular characterization of resistance determinants and strain typing. In order to gain a better understanding of the circulating sequence types (STs) and resistance determinants in cases where specimens are not collected for culture, such as community patients, a more practical approach would be to test the original sample submitted for Aptima testing by molecular methods. Methods Sample pairs (specimen submitted for Aptima testing and culture within one day) from 26 patients including 22 males and 4 females ranging in age from 20 to 59 years were extracted using the QIAamp DNA mini kit and compared for direct molecular characterization. Samples were analysed for antimicrobial susceptibility based on mosiac changes that have been correlated with reduced susceptibility to extended-spectrum cephalosporins (ESCrs) in the PBP2 protein coded by penA. Outer membrane proteins PIA and PIB coded by porA/B and tbpB genes were sequenced and multiantigen sequence typing (NG-MAST) was performed. Results 100% sequence identity was observed between the sequences obtained from the Aptima and culture samples suggeting that direct molecular characterization can be performed from Aptima specimens. Based on the sequence data a strong correlation was observed between ESCrs, tbp allele 110, ST1407 and amino acid changes (G545S, I312M, V316T) in the PBP2 protein. Conclusions This strategy will provide comprehensive surveillance data on circulating NG strains in lower risk populations and may help in guiding empiric treatment. Molecular methods can be enhanced for high throughput characterization of community 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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 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) | 0.006 | 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".