{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009880017,0.0002699046,0.0002805111,0.00003530228,0.000250634,0.0001421899,0.00009210607,0.00007782412,0.000008883488],"category_scores_gemma":[0.0001452184,0.000125727,0.00007995918,0.0003108966,0.00005339553,0.00009005312,0.00005220354,0.000119611,0.000001898913],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002701015,"about_ca_system_score_gemma":0.0002463151,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.02732659,"about_ca_topic_score_gemma":0.1121544,"domain_scores_codex":[0.9981219,0.0003254609,0.000308859,0.000683455,0.0001716092,0.0003886965],"domain_scores_gemma":[0.9986883,0.000693864,0.00005641951,0.00009130962,0.00006315059,0.0004069059],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.004066009,0.00003249461,0.007719155,0.00006654226,0.00003377837,0.00003925989,0.0004930896,0.001739603,0.9780723,0.00001196015,0.0005613936,0.007164351],"study_design_scores_gemma":[0.0006266448,0.0009704567,0.9815072,0.0001073816,0.0000591753,0.00004497742,0.001266298,0.00641688,0.001424142,0.000565633,0.00634192,0.0006693215],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9884776,0.002759363,0.0000480583,0.005647846,0.0001564431,0.0006211558,0.002242096,0.0000252951,0.00002214099],"genre_scores_gemma":[0.9962595,0.0001703709,0.00002304635,0.003022232,0.0002531499,0.0001056489,0.0001394363,0.000006344888,0.00002029542],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9766482,"threshold_uncertainty_score":0.9791505,"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."}}