Examining Heterogeneity in the Diagnostic Accuracy of Culture and PCR for<i>Salmonella</i>spp. in Swine: A Systematic Review/Meta‐Regression Approach
Bibliographic record
Abstract
The accuracy of bacterial culture and PCR for Salmonella in swine was examined through systematic review of existing primary research in this field. A replicable search was conducted in 10 electronic databases. All steps of the review were conducted by two reviewers: to identify relevant publications, to assess their methodological soundness and reporting, and to extract raw data or reported test accuracy estimates. Meta-analyses and meta-regression were performed: to evaluate pooled estimates of test sensitivity (Se) and specificity (Sp), to identify variables explaining the variation in reported test estimates, and to evaluate the association between these variables and reported test Se and Sp. Twenty-nine studies were included in the review. Unique test evaluations reported in these 29 studies were categorized according to the type of test comparison: culture versus culture (n = 134 test evaluations) and PCR versus culture (n = 21). We identified significant heterogeneity among evaluations for each test category. For culture, more heterogeneity was caused by differences in individual test protocols (52%) than overall differences between studies (16%). Enrichment temperature, study population, agar and enrichment type were significantly associated with variation in culture Se. Furthermore, interaction between enrichment temperature and enrichment type was detected. For PCR, most of the heterogeneity was caused by overall differences between studies (65-70%); sample type and study size were associated with variation in reported PCR Se and Sp. The overall methodological soundness and/or reporting of primary studies included in this review were poor, with variable use of reference standards, and consistent lack of the use or reporting of blinding, randomization and subject (sample) selection criteria. Consequently, the food safety and veterinary public health research community should formally consider ways for standardizing the conduct and reporting of this type of research.
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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 | 0.005 | 0.004 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.004 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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".