{"id":"W2901663682","doi":"10.1186/s13756-018-0437-7","title":"Investigation of a Carbapenemase-producing Acinetobacter baumannii outbreak using whole genome sequencing versus a standard epidemiologic investigation","year":2018,"lang":"en","type":"article","venue":"Antimicrobial Resistance and Infection Control","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":23,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Ste. Anne's Hospital; University of Northern British Columbia; Manitoba Beekeepers' Association; University of Manitoba","funders":"Fonds de Recherche du Québec - Santé","keywords":"Concordance; Outbreak; Whole genome sequencing; Pulsed-field gel electrophoresis; Acinetobacter baumannii; Transmission (telecommunications); Acinetobacter; Medicine; Genome; Biology; Virology; Genetics; Genotype; Computer science; Internal medicine; Bacteria; Gene; Pseudomonas aeruginosa","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006291335,0.0002305951,0.0003603311,0.00009543718,0.0002369341,0.00004909567,0.00009125996,0.0002090046,0.00001105126],"category_scores_gemma":[0.0004702653,0.0002276996,0.00008796227,0.0001776895,0.0004930136,0.00004670614,0.00004986549,0.0001062113,0.000004080065],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001031786,"about_ca_system_score_gemma":0.0001957718,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001964965,"about_ca_topic_score_gemma":0.0006999719,"domain_scores_codex":[0.998338,0.0002098185,0.0005114545,0.0005285867,0.0001163336,0.0002957791],"domain_scores_gemma":[0.9987304,0.00004753936,0.0004228014,0.0003408321,0.0003719157,0.00008646472],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001125475,0.000003811391,0.05497315,0.00008320899,0.00007002275,8.507342e-7,0.0001101492,0.00006874127,0.9430785,0.00004137304,0.000373937,0.00007084218],"study_design_scores_gemma":[0.004538537,0.00118628,0.1544587,0.0004418403,0.0002238793,0.00001953103,0.00008739849,0.0003688719,0.8317558,0.0002386229,0.005998198,0.0006822678],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9919599,0.0001942941,0.006701733,0.0001814224,0.0003864272,0.0003270009,0.00006711361,0.00002478544,0.0001573055],"genre_scores_gemma":[0.996466,0.0001279584,0.002152792,0.0004237319,0.0005722742,0.000004972935,0.0001073838,0.00002627958,0.000118551],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1113226,"threshold_uncertainty_score":0.9285321,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02961240521720541,"score_gpt":0.2671481301583156,"score_spread":0.2375357249411102,"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."}}