The application of deep amplicon sequencing to the diagnostics and molecular epidemiology of anthelmintic resistance in sheep gastrointestinal nematodes
Bibliographic record
Abstract
Gastrointestinal nematodes (GIN) are a major challenge for sheep producers worldwide. They cause a variety of clinical signs and large economic impact. Anthelmintics are commonly used in control, however, indiscriminate use of these drugs over many years has led to the problem of anthelmintic resistance. The lack of accurate resistance diagnostic methods increases the challenge of parasite control. This thesis investigates the problem of anthelmintic resistance in Western Canadian sheep for the first time. This region has been believed unsuitable for GIN due to suboptimal weather and low treatment selection pressure. Chapter 2 presents a large-scale survey of anthelmintic efficacy. The precision of the Fecal Egg Count Reduction Test (FECRT) diagnostic method was also investigated. Results revealed high GIN infection intensity and anthelmintic resistance against benzimidazoles and ivermectin, highlighting the urgent need for better diagnostic tools. Chapter 3 validates the recently developed nemabiome metabarcoding approach for the relative quantitation of GIN species in ovine fecal samples. Chapter 4 applies the validated approach integrated to FECRT to a large-scale study in Western Canada and revealed widespread resistance of H. contortus to benzimidazoles and ivermectin. Resistance to closantel was absent, but this drug was often ineffective due to its narrow spectrum activity.Chapter 5 applies deep amplicon sequencing to screen for benzimidazole resistance mutations in the isotype-1 b-tubulin gene of the main GIN in Western Canada and United States of America (USA). Codon F200Y(TTC>TAC) mutation was found at high frequency in H. contortus and at lower frequencies in other species. The relative frequencies of resistance mutations were similar between Western Canada and USA, although generally higher in USA, consistent with greater selection pressure. A pilot study also identified resistance mutations in the isotype-2 b-tubulin gene of H. contortus, suggesting this locus warrants further investigation regarding its role in benzimidazole resistance. Phylogenetic network analysis revealed that the most common resistance haplotypes were shared between Western Canada and USA, supporting a hypothesis of common origins of resistance. Given the more advanced resistance in the USA, a likely scenario is that anthelmintic resistant parasites were introduced to Western Canada from sheep imported from the USA.
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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 | 0.001 | 0.003 |
| 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) | 0.000 | 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".