{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.009923968,0.0001692505,0.001262299,0.00003481712,0.00009746334,0.0000176074,0.0007045735,0.0002095565,0.00001396569],"category_scores_gemma":[0.002721617,0.0000479525,0.0005018065,0.000459983,0.001318163,0.00005277354,0.0001405443,0.0003710253,8.322017e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002125532,"about_ca_system_score_gemma":0.00005844144,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006326259,"about_ca_topic_score_gemma":0.0008363227,"domain_scores_codex":[0.9940898,0.002821999,0.002473533,0.0002511695,0.0001073104,0.0002562317],"domain_scores_gemma":[0.985018,0.01205151,0.002203299,0.0001671999,0.0004590738,0.0001009094],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.007570528,0.001518676,0.6607835,0.00006705643,0.002655251,0.00001473805,0.00265674,0.0004594579,0.3048486,0.01031264,0.001291675,0.007821216],"study_design_scores_gemma":[0.002920679,0.001623157,0.9780694,0.00004211635,0.0007398473,0.0001773302,0.002219838,0.00008734692,0.0005717767,0.007706186,0.00566726,0.0001750793],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9843137,0.0006188722,0.0001339385,0.01408711,0.0003163018,0.0003406324,0.0001720934,0.000003069668,0.00001427759],"genre_scores_gemma":[0.9967996,0.0002121914,0.0002902118,0.002311265,0.000318202,0.000008719073,0.00004599265,0.000001712486,0.0000121228],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3172859,"threshold_uncertainty_score":0.4856828,"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."}}