{"id":"W3214279010","doi":"10.1371/journal.pone.0260234","title":"Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada","year":2021,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; Public Health Agency of Canada","funders":"Ontario Ministry of Agriculture, Food and Rural Affairs; Public Health Agency; Public Health Agency of Canada; Ontario Agri-Food Innovation Alliance; University of Guelph","keywords":"Salmonella; Manure; Biology; Veterinary medicine; Escherichia coli; Antibiotic resistance; Whole genome sequencing; Antimicrobial; Microbiology; Genome; Bacteria; Genetics; Agronomy; Antibiotics; Medicine; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003221145,0.0003225275,0.0002670086,0.001389163,0.0007571432,0.0005834244,0.0003353099,0.0002052441,0.0004421041],"category_scores_gemma":[0.0008750936,0.0001974757,0.000309737,0.002890021,0.0003580099,0.0001414109,0.0003401797,0.0002310954,0.00008448929],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.005420425,"about_ca_system_score_gemma":0.006783279,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.9538835,"about_ca_topic_score_gemma":0.9854398,"domain_scores_codex":[0.999615,0.00002812016,0.00002013872,0.000108952,0.0001275087,0.0001002483],"domain_scores_gemma":[0.9991615,0.00007563731,0.0002168851,0.00003400928,0.0003655062,0.0001464966],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00007872358,0.00001624954,0.9851211,0.00004343812,0.00007014506,0.0001473269,0.0009401672,0.0003280713,0.00952382,0.00002418719,0.0001795547,0.003527177],"study_design_scores_gemma":[0.000001608809,0.00001159963,0.9991129,0.000004470795,0.000008758218,0.00002442794,0.0003563184,0.0001323575,0.0001052488,0.000002101704,0.0002382858,0.000001793402],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975641,0.0001104855,0.0001316626,0.00001482662,8.972925e-7,0.00002098821,0.001877492,0.000003433928,0.0002761838],"genre_scores_gemma":[0.9927022,0.0002473418,0.00105026,0.00003569316,0.000001513707,0.00002393626,0.00530196,0.000003960578,0.0006331228],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04611647,"threshold_uncertainty_score":0.09277606,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1821881773263866,"score_gpt":0.2637576092059961,"score_spread":0.08156943187960947,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}