Investigation of the distribution and risk factors associated with Mycobacterium avium subspecies paratuberculosis in cow-calf herds in Canada
Bibliographic record
Abstract
This thesis summarizes an investigation of Mycobacterium avium subspecies paratuberculosis (Map) as a pathogen within the cow-calf industry in Canada. The specific objectives of this project were to describe the distribution of this pathogen in this industry provincially, as well as at the individual farm level in wildlife species, and in the environment. Secondary objectives of this project were to identify on-farm management risk factors that are associated with this disease and to examine potential options for herd level diagnostic capabilities. Nationally, 0.8% (95%CI = 0.4-1.1%) of the cows in the cow-calf industry were seropositive for Map with 11.7% (95%CI=7.0-16.5%) of the herds sampled having a minimum of one positive test result or 4.5% (95%CI=1.4-7.5%) of the herds having a minimum of two positive test results. The true cow prevalence was estimated as 1.8% (95%CI= 0.4 – 3.1). No Map was detected in any of the non-ruminant wildlife species sampled on cow-calf operations suggesting that these species were not of primary concern when dealing with the management of this disease. In a study not focussed on a cow-calf operation, Map was detected in one cluster of trapped coyote samples in a region with cow-calf production. The prevalence of Map infection in this cluster of coyotes was calculated to be 9.1% (CI: 5.7-12.5). The prevalence of infection in coyotes including all sites, ignoring the effect of clustering, was calculated to be 3.7% (CI: 2.3-5.1). The use of a commercial colostrum replacement on farm (Odds Ratio =3.96; 95% CI = 1.10–14.23, p=0.035) and the presence of wild deer interacting with the cattle (Odds Ratio = 14.32; 95% CI = 1.13–181.90, p=0.040) were positively associated with being a herd infected with paratuberculosis. The use of rotational grazing practices was protective (Odds Ratio = 0.20; 95% CI = 0.04–0.93, p=0.039). It was possible to detect environmental contamination with Map on cow-calf farms using bacterial culture and PCR for confirmation. No water samples were positive to Map; however, 6.2% of the non-water environmental samples were positive. The use of an environmental sampling protocol had a herd sensitivity of 29.6%. This finding led to a simulation modelling study to evaluate how various testing methods would compare in the broader population of cow-calf herds. The final mean risk of selecting a herd infected with Map that was not identified as positive via the herd screen test strategy was 12.9%, 9.8%, 9.6%, and 6.1% for no herd screen test, environmental sampling, ELISA serology, and pooled fecal culture strategies, respectively.
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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 | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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 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".