{"id":"W2908694387","doi":"10.1099/mgen.0.000237","title":"Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria","year":2019,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Listeria monocytogenes in Food Safety","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ste. Anne's Hospital; University of Guelph; BC Centre for Disease Control; Public Health Ontario; Health Canada; Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada; Canadian Food Inspection Agency","keywords":"Subtyping; Genome; Biology; Phylogenetic tree; Outbreak; Prophage; Genetics; Whole genome sequencing; Phylogenetics; Evolutionary biology; Virology; Gene; Bacteriophage","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":[0.009431633,0.000778485,0.0008104348,0.004125018,0.001270635,0.00344699,0.001287298,0.0008771335,0.001430492],"category_scores_gemma":[0.02791966,0.0004160933,0.001048449,0.005599451,0.001050398,0.001065117,0.003216868,0.001019396,0.0003378562],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00249112,"about_ca_system_score_gemma":0.003603469,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0367457,"about_ca_topic_score_gemma":0.09903729,"domain_scores_codex":[0.9922069,0.003025454,0.0007736077,0.001802775,0.001589658,0.0006016532],"domain_scores_gemma":[0.9805644,0.00901886,0.002649232,0.003943008,0.003249159,0.0005753617],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001372609,0.0002114404,0.7780783,0.002361096,0.003046667,0.001635242,0.005087909,0.01496626,0.07188018,0.00747291,0.003903916,0.1099833],"study_design_scores_gemma":[0.00005090422,0.0001542408,0.949328,0.0003788793,0.0005954294,0.0008763021,0.002721136,0.01302564,0.007661012,0.007182001,0.01795161,0.00007478868],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9039,0.002876548,0.0516984,0.001374466,0.00007878588,0.0002755105,0.03215154,0.000685561,0.006959142],"genre_scores_gemma":[0.9249597,0.0004662039,0.04645746,0.0002875655,0.0000299411,0.0001336033,0.02698612,0.0002118126,0.000467471],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0367457,"threshold_uncertainty_score":0.07306361,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1004484279472736,"score_gpt":0.3800535996092121,"score_spread":0.2796051716619385,"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."}}