Laboratory Performance and Clinical Correlation of Real-time Polymerase Chain Reaction as a Diagnostic Test for Bordetella Pertussis Isolated from Patients in Oman
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Bibliographic record
Abstract
Objectives: To evaluate real-time polymerase chain reaction (PCR) as a diagnostic tool for pertussis (whooping cough), vis-à-vis culture, the long-time gold standard, with emphasis on the importance of clinical correlation in determining specificity. Methods: Nasopharyngeal/throat swab samples in charcoal media received from all over Oman at Central Public Health Laboratories from January 2014 to December 2016 were included in this study. These samples were tested using both culture and real-time PCR. PCR was compared with culture to calculate its sensitivity and specificity. Further clinical correlation was conducted for the discrepant cases using different case definitions. Results: A total of 590 nasopharyngeal/throat samples were included in the study. Out of the 590 samples, 73 were positive by PCR compared with 26 positive samples by culture (which were also positive by PCR). The sensitivity and specificity of PCR compared with those of culture were 100% (95% CI: 86.77-100) and 91.7% (95% CI: 89.07-93.81), respectively. To rule out false-positive results by PCR, clinical correlation was performed. Out of 47 cases that were positive by PCR but negative by culture, 44 cases were clinically evaluated by accessing clinical details. Out of these 44 cases, 21 (47.7%) met the pertussis clinical criteria according to the CDC-2014 case definition, 41 (93.2%) according to the Europe-2008 case definition, and 44 (100%) according to the Canada-2009 and Australia-2014 case definitions. With only positive PCR, these cases were classified as confirmed according to these case definitions, which increased the specificity of PCR to 95.7-100%. The mean turnaround time was 3.5 days for PCR compared to 6.2 days for culture. Conclusions: infection. Based on our results, we recommend setting up PCR diagnostic facilities in regional hospitals in Oman as this will lead to a timely and accurate diagnosis of pertussis.
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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 | 0.004 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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 it