{"id":"W4400641612","doi":"10.1101/2024.02.22.24302918","title":"Genomic reconstruction of an azole-resistant <i>Candida parapsilosis</i> outbreak and the creation of a multilocus sequence typing scheme: a retrospective observational and genomic epidemiology study","year":2024,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Antifungal resistance and susceptibility","field":"Medicine","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Bundesministerium für Bildung und Forschung; Robert Koch Institut; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Deutsche Forschungsgemeinschaft; Friedrich-Schiller-Universität Jena; Pfizer","keywords":"Candida parapsilosis; Multilocus sequence typing; Typing; Epidemiology; Molecular epidemiology; Biology; Genetics; Outbreak; Genotyping; Medicine; Virology; Gene; Genotype; Candida albicans; Internal medicine","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006784556,0.0002585151,0.0002562032,0.000911778,0.0003723007,0.0007342086,0.0003643479,0.0004819562,0.0005839769],"category_scores_gemma":[0.001983677,0.0003872139,0.0003911975,0.000898517,0.0004627778,0.000437778,0.00060729,0.0003511958,0.0001231233],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005200018,"about_ca_system_score_gemma":0.0004325628,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006669636,"about_ca_topic_score_gemma":0.00528061,"domain_scores_codex":[0.9994329,0.0001321491,0.00006355379,0.0002084855,0.00006616829,0.00009683148],"domain_scores_gemma":[0.9982076,0.0002644798,0.0009181414,0.0002306647,0.0001415973,0.0002375097],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0000496385,0.00002208838,0.9987858,0.000005360411,0.0000321281,0.0001688334,0.0001118161,0.00004373461,0.0002672899,0.00001844284,0.00005064081,0.0004442454],"study_design_scores_gemma":[0.000004896936,0.00009600075,0.9978807,0.000007385541,0.00003874355,0.000831784,0.0004289288,0.0003884858,0.0001148303,0.00002449305,0.0001784152,0.000005314195],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9995988,0.00003433532,0.0001155564,0.00001104651,0.000001032785,0.00000551388,0.0001698891,0.000001356372,0.00006251392],"genre_scores_gemma":[0.9995147,0.00003435117,0.0001271827,0.00001300684,0.0000032552,0.000004496878,0.0002836768,0.000001288984,0.00001815471],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006669636,"threshold_uncertainty_score":0.01326162,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06568213023926765,"score_gpt":0.3427949126182749,"score_spread":0.2771127823790073,"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."}}