{"id":"W4404420763","doi":"10.1016/j.lanmic.2024.07.012","title":"Genomic reconstruction of an azole-resistant Candida parapsilosis outbreak and the creation of a multi-locus sequence typing scheme: a retrospective observational and genomic epidemiology study","year":2024,"lang":"en","type":"article","venue":"The Lancet Microbe","topic":"Antifungal resistance and susceptibility","field":"Medicine","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Candida parapsilosis; Typing; Locus (genetics); Epidemiology; Outbreak; Genetics; Biology; Molecular epidemiology; Medicine; Virology; Gene; Candida albicans; Internal medicine; Genotype","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":[0.001291182,0.0002863824,0.0003405913,0.00135275,0.0005003509,0.0007663815,0.0004868999,0.0006605127,0.0005584179],"category_scores_gemma":[0.004506208,0.0005077653,0.0004456479,0.001524622,0.0004906237,0.0004672298,0.0009285246,0.0005250106,0.0001426426],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005428699,"about_ca_system_score_gemma":0.00059723,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.008191752,"about_ca_topic_score_gemma":0.007385686,"domain_scores_codex":[0.9989311,0.0003232764,0.0001091578,0.000371516,0.0001143309,0.0001506062],"domain_scores_gemma":[0.9971276,0.0005570931,0.001166409,0.0004882427,0.0003079041,0.0003527568],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.000118267,0.00004997777,0.9974878,0.00001321937,0.00006929951,0.0003029619,0.0003174729,0.0001604972,0.0003898889,0.00005806149,0.0001483378,0.0008842869],"study_design_scores_gemma":[0.00001166695,0.0001667235,0.9958955,0.00002049519,0.00006918717,0.001081133,0.0008172499,0.001240453,0.000138776,0.00008909304,0.0004577428,0.00001191464],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9988845,0.00006039773,0.000364697,0.00002519246,0.000002041094,0.00001476022,0.0005566148,0.000002562001,0.00008929185],"genre_scores_gemma":[0.9983212,0.00006470335,0.0005506091,0.00002799421,0.000004894363,0.00001470849,0.0009789674,0.000003401963,0.000033499],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.008191752,"threshold_uncertainty_score":0.01628816,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09159180753223989,"score_gpt":0.3530257215701824,"score_spread":0.2614339140379425,"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."}}