Utilization of Nucleic Acid Amplification Testing Samples for Antimicrobial Resistance Surveillance in Remote Canadian Communities
Bibliographic record
Abstract
Dear Editor: We have read the article by Thakur et al.1 with great interest. We agree with their general statement that Neisseria gonorrhoeae diagnosis continues to expand to non–culture-based methods directly from clinical specimens. There is a need to use remnants of existing nucleic acid amplification testing (NAAT) samples generated from frontline laboratories for N. gonorrhoeae to predict antimicrobial resistance and generate a molecular type to track the dissemination of strains for surveillance and public health response. To this end, the Public Health Agency of Canada has developed real-time polymerase chain reaction (RT-PCR) assays to predict the presence of antimicrobial resistance markers and PCR sequence analysis to generate an Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) directly from NAAT specimens. Specifically, we have developed RT-PCR assays to detect mutations associated with ciprofloxacin and cephalosporin resistance directly from residual NAAT specimens with high degrees of sensitivity and specificity when compared with culture.2,3 In addition, we have adopted an existing RT-PCR protocol for the detection of azithromycin-resistant mutations.4 Finally, we have validated these methods along with the molecular typing of NG-MAST from NAAT specimens with matched clinical isolates using traditional antimicrobial resistance and NG-MAST testing of the clinical isolate.5 In remote northern parts of Canada, it is very difficult to obtain specimens that have viable N. gonorrhoeae due to cold temperatures and the time it takes to transport a specimen to a laboratory with the expertise to culture an isolate. We are using our RT-PCR assays and NG-MAST typing assay to establish molecular antimicrobial resistance surveillance in remote northern communities. We believe that this is the first step in using molecular methods to predict and type N. gonorrhoeae for antimicrobial resistance surveillance and public health interventions. The NG-MAST typing data will also aid in identifying transmission patterns, which will hopefully lead to interventions to limit the dissemination of N. gonorrhoeae in these remote communities. In conclusion, we believe that the molecular detection of antimicrobial resistance genes and the typing of N. gonorrhoeae directly from NAATs will expand the availability of the much-needed information to remote communities where culture is not possible. Finally, we continue to explore methods to generate whole-genome sequence data from either NAAT or urine specimens. We believe that this is the future of the technology as our recent collaborations have shown that the use of whole-genome sequence can accurately predict not only susceptible/intermediate/resistant interpretations but also minimum inhibitory concentrations for specific antimicrobials.6 Michael R. MulveyIrene Martin Public Health Agency of Canada Winnipeg, Manitoba Canada [email protected]Tom Wong First Nations and Inuit Health Branch Ottawa, Ontario Canada
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 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".