{"id":"W2219221016","doi":"10.1128/jcm.02200-15","title":"Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations","year":2015,"lang":"en","type":"article","venue":"Journal of Clinical Microbiology","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":80,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ministère de l'Agriculture, des Pêcheries et de l'Alimentation; Ministère de la Santé et des Services Sociaux (Québec); Université de Montréal; Santé Montérégie; McGill University; Public Health Agency of Canada; Institut National de Santé Publique du Québec","funders":"","keywords":"Subtyping; Pulsed-field gel electrophoresis; Outbreak; Salmonella enterica; Serotype; Biology; Genome; Phylogenetic tree; Pathogenicity island; Context (archaeology); Typing; Salmonella; Genetics; Molecular epidemiology; Virology; Genotype; Gene; Bacteria","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0009741831,0.0004481956,0.0003745672,0.001387743,0.0006034778,0.001317099,0.0004118528,0.0003084072,0.001000499],"category_scores_gemma":[0.002332558,0.0001648846,0.0003779941,0.00160733,0.0002773056,0.0003208453,0.0004317385,0.0002492216,0.0003500554],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001285957,"about_ca_system_score_gemma":0.002101335,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.2428769,"about_ca_topic_score_gemma":0.4105867,"domain_scores_codex":[0.9995183,0.00007380387,0.00003319129,0.0001473047,0.0001574553,0.00006996405],"domain_scores_gemma":[0.9986836,0.0002841584,0.0002084758,0.0001019548,0.0006088227,0.0001129445],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0009588249,0.0001462861,0.506318,0.0005812315,0.0003956045,0.0008974952,0.00131624,0.008590695,0.4048033,0.0004716527,0.002608242,0.07291242],"study_design_scores_gemma":[0.00002249634,0.000180093,0.9253057,0.0001036038,0.0002574699,0.0005660459,0.001060915,0.03332749,0.03078921,0.0002243999,0.008097886,0.00006463753],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9743726,0.0006159051,0.01304626,0.0001228414,0.00001525089,0.00009606449,0.009365794,0.0003514681,0.002013822],"genre_scores_gemma":[0.9648952,0.0002931401,0.02386916,0.00009407114,0.000006253101,0.00002828131,0.01020372,0.00008437164,0.0005257982],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2428769,"threshold_uncertainty_score":0.4829265,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1754584784246452,"score_gpt":0.3401878660630401,"score_spread":0.1647293876383949,"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."}}