{"id":"W4401390971","doi":"10.1089/fpd.2024.0041","title":"Transition to Whole Genome Sequencing Surveillance: The Impact on National Outbreak Detection and Response for <i>Listeria monocytogenes</i> , <i>Salmonella</i> , Shiga Toxin–Producing <i>Escherichia coli</i> , and <i>Shigella</i> Clusters in Canada, 2015–2021","year":2024,"lang":"en","type":"article","venue":"Foodborne Pathogens and Disease","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada","keywords":"Listeria monocytogenes; Salmonella; Outbreak; Shigella; Escherichia coli; Microbiology; Biology; Listeria; Foodborne pathogen; Shiga toxin; Virology; Bacteria; Genetics; 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":[0.002287847,0.0003191872,0.0001993473,0.0007010491,0.0007858303,0.001239265,0.0008540245,0.00049315,0.0010923],"category_scores_gemma":[0.005072148,0.0002013083,0.0003687495,0.0009793004,0.0004475782,0.000504738,0.0007104097,0.0006409144,0.0001260776],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.02520545,"about_ca_system_score_gemma":0.07737879,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.9832706,"about_ca_topic_score_gemma":0.9862071,"domain_scores_codex":[0.9986285,0.0001856052,0.00005301374,0.0001826881,0.0004600799,0.0004901495],"domain_scores_gemma":[0.9959866,0.0003144119,0.0002849816,0.00008347547,0.002123391,0.001207135],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001840994,0.0003056162,0.7732298,0.0007631495,0.00022439,0.0003211091,0.00268278,0.01006498,0.01231667,0.001438989,0.03234929,0.1644622],"study_design_scores_gemma":[0.00003111911,0.0001610819,0.9843565,0.0001154373,0.00004035342,0.00003990319,0.001606364,0.004203382,0.001303242,0.0001237532,0.007996146,0.00002276694],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9648551,0.001899112,0.001983898,0.008463072,0.0001180711,0.000318147,0.01502425,0.0002968113,0.007041518],"genre_scores_gemma":[0.9838847,0.001190356,0.004296464,0.002038855,0.00002474664,0.00007063005,0.00641774,0.00002183866,0.002054649],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02520545,"threshold_uncertainty_score":0.1828792,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02129424159898351,"score_gpt":0.2493071771818712,"score_spread":0.2280129355828877,"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."}}