{"id":"W2909238093","doi":"10.1101/521260","title":"Genomic and epidemiological evidence of a dominant Panton-Valentine leucocidin-positive Methicillin Resistant <i>Staphylococcus aureus</i> lineage in Sri Lanka with spread to the United Kingdom and Australia","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Antimicrobial Resistance in Staphylococcus","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Fleming College","funders":"National Institute of Allergy and Infectious Diseases; National Institutes of Health; Universidad de Buenos Aires; Wellcome Trust; Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS)","keywords":"Multilocus sequence typing; Sri lanka; Methicillin-resistant Staphylococcus aureus; Staphylococcus aureus; Lineage (genetic); Panton–Valentine leukocidin; Phylogenetic tree; SCCmec; Molecular epidemiology; Typing; Medicine; Microbiology; Biology; Veterinary medicine; Genotype; Genetics; Gene; Geography; Bacteria","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"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":[0.0002039819,0.0002947061,0.000224008,0.001256629,0.0004030012,0.0006322797,0.0002913426,0.0003685531,0.001464993],"category_scores_gemma":[0.0009391687,0.0003611811,0.0002746463,0.001136732,0.0005380458,0.0002898213,0.0004964581,0.0003062521,0.0002200774],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004334379,"about_ca_system_score_gemma":0.0004405722,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.03178435,"about_ca_topic_score_gemma":0.02698382,"domain_scores_codex":[0.9995996,0.00008155832,0.0000575083,0.0001144933,0.00005357966,0.00009318873],"domain_scores_gemma":[0.9988074,0.0001240991,0.0005669566,0.00005714244,0.0002371107,0.0002073233],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00005097561,0.00001293612,0.992705,0.00002990198,0.00003118458,0.0008356547,0.0004387436,0.00002809498,0.004135878,0.00001295143,0.00005149166,0.00166726],"study_design_scores_gemma":[0.000001791474,0.00005618388,0.9981753,0.000007428465,0.00001527059,0.001006656,0.0005455558,0.00002490659,0.00008228173,0.000003156089,0.00007889808,0.000002564463],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9994874,0.0001079304,0.00004613671,0.00001929908,7.681853e-7,0.000006322142,0.00009478979,0.000001874653,0.0002354877],"genre_scores_gemma":[0.9996812,0.00009460088,0.00007158666,0.00001106754,0.000001980724,0.000003394243,0.00009141913,6.619377e-7,0.00004401066],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03178435,"threshold_uncertainty_score":0.06319869,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05360604225196291,"score_gpt":0.3029000900322192,"score_spread":0.2492940477802563,"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."}}