Evaluation of the reproducibility and performance characteristics of the Phagomagnetic separation-qPCR assay for rapidly detecting viable Mycobacterium avium subsp. paratuberculosis in bovine milk and feces
Bibliographic record
Abstract
(MAP) in bovine milk and feces. Unique reagents and a detailed instruction manual required for the PhMS-qPCR assay were provided to five European veterinary diagnostic laboratories by Rapid-Myco Technologies Limited. Milk and feces test panels were prepared at NEIKER and distributed to participant laboratories between April-June 2023 and March-May 2024, respectively. Each test panel comprised of MAP-spiked and/or naturally infected bovine milk or feces samples (18 samples per panel on two separate occasions for each sample matrix). The six participant laboratories (including organizer) performed automated or manual PhMS and used whatever qPCR instrument they had available. All laboratories used the IDEXX RealPCR MAP DNA test for the qPCR part of the assay. Generally, substantial agreement was observed overall between PhMS-qPCR results and reference culture results for spiked milk (Kappa value 0.5982) and naturally MAP-infected feces (Kappa value 0.7780 using an amended protocol). Preliminary estimates of the detection (analytical) sensitivity (Se), detection specificity (Sp) and trueness (T) of the PhMS-qPCR assay applied to bovine milk and feces were obtained. The mean Se, Sp, and T values across six laboratories were 93.1%, 67.9%, and 88.7% when milk was tested and 84.1%, 93.7%, and 88.9% when feces was tested. Overall, the PhMS-qPCR assay performed well in multiple laboratories and test reproducibility was demonstrated (Cohen's Kappa ≥0.6-1.000). The estimates of performance characteristics of the PhMS-qPCR assay are generally acceptable for a potential diagnostic test. Hence the PhMS-qPCR assay shows considerable promise as a rapid test to detect viable MAP in veterinary specimens such as milk and feces. Further and fuller validation of the assay will continue to assess its diagnostic potential.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.050 | 0.056 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 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) | 0.001 | 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".