{"id":"W4210812290","doi":"10.1038/s41467-022-28156-4","title":"Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings","year":2022,"lang":"en","type":"article","venue":"Nature Communications","topic":"Antimicrobial Resistance in Staphylococcus","field":"Medicine","cited_by":75,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Medical Research Council; National Health and Medical Research Council; State Government of Victoria; Peter MacCallum Cancer Centre; Monash University; University of Toronto; U.S. Department of Health and Human Services","keywords":"Enterococcus faecium; Transmission (telecommunications); Genomics; Genome; Multilocus sequence typing; Biology; Genotyping; Computational biology; Population; Population genomics; Genetics; Medicine; Computer science; Genotype; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007266423,0.0002094419,0.0003829564,0.0003510644,0.0009575419,0.00004545011,0.0009399753,0.0001987377,0.00002234421],"category_scores_gemma":[0.0001242398,0.0002256814,0.0002069451,0.0006200295,0.0001026715,0.0000960552,0.0004351161,0.001883132,0.00000197439],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000744659,"about_ca_system_score_gemma":0.0002549171,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000667062,"about_ca_topic_score_gemma":0.0002865799,"domain_scores_codex":[0.9980797,0.0002286965,0.0005529906,0.0004072826,0.0003167426,0.0004146229],"domain_scores_gemma":[0.9977386,0.0003645571,0.0002168065,0.001418453,0.0001334078,0.0001281568],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.007143321,0.0047673,0.04498422,0.004192272,0.0006924708,0.0001008599,0.01643145,0.002759617,0.7531417,0.03560693,0.04300116,0.08717871],"study_design_scores_gemma":[0.00911683,0.000636577,0.07248574,0.001321412,0.0004609971,0.0001140299,0.008386018,0.01289776,0.006369668,0.002225684,0.8847145,0.001270749],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5979951,0.1444999,0.02264298,0.21445,0.001207152,0.0129212,0.001045365,0.0007044296,0.004533899],"genre_scores_gemma":[0.9374136,0.0003276742,0.05959192,0.001507433,0.00004156808,0.0004473975,0.0004109941,0.00005778588,0.0002015838],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8417134,"threshold_uncertainty_score":0.920302,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07040425077968182,"score_gpt":0.3475669095589191,"score_spread":0.2771626587792372,"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."}}