{"id":"W4404852518","doi":"10.1128/spectrum.01366-24","title":"Rapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbor typing","year":2024,"lang":"en","type":"article","venue":"Microbiology Spectrum","topic":"Bacterial Identification and Susceptibility Testing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Sinai Health System; University Health Network; University of Toronto; Canadian Electricity Association; Canada Research Chairs; Ottawa Hospital","funders":"Canadian Institutes of Health Research; Joint Programming Initiative on Antimicrobial Resistance; Pfizer","keywords":"Multilocus sequence typing; Metagenomics; Typing; Biology; Genetics; Computational biology; Microbiology; Genotype; Gene","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002474935,0.0005998562,0.0007986736,0.001701836,0.0001935489,0.001139679,0.0005513892,0.0005445801,0.0005736235],"category_scores_gemma":[0.006596224,0.0004189764,0.0007911413,0.0007877219,0.0002163864,0.0006290792,0.0007241585,0.0005327927,0.0003770897],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003003889,"about_ca_system_score_gemma":0.0002689807,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001459062,"about_ca_topic_score_gemma":0.002154512,"domain_scores_codex":[0.9982002,0.0006961707,0.0001528666,0.000514544,0.0003534727,0.00008274105],"domain_scores_gemma":[0.9964699,0.001991127,0.0006345885,0.0003752917,0.0004034879,0.0001256479],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001219786,0.0002562663,0.6209291,0.0003988504,0.0007586514,0.0003130959,0.0003171396,0.02339563,0.2549685,0.00078808,0.0004738639,0.09618109],"study_design_scores_gemma":[0.00007053339,0.0006480157,0.1887353,0.0001598091,0.000499325,0.001154727,0.0004070476,0.6939248,0.1083547,0.003370309,0.002544925,0.0001304558],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8484344,0.0008885234,0.1463465,0.0001635147,0.0000378778,0.0001400049,0.002383755,0.0006369365,0.0009685284],"genre_scores_gemma":[0.8995779,0.0001611411,0.0988537,0.00007599458,0.00001477773,0.00003826331,0.001061044,0.00005649975,0.0001606089],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002474935,"threshold_uncertainty_score":0.01308888,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02529019211393944,"score_gpt":0.2610753273652527,"score_spread":0.2357851352513133,"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."}}