{"id":"W4213178920","doi":"10.3390/microorganisms10020441","title":"Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool","year":2022,"lang":"en","type":"article","venue":"Microorganisms","topic":"Probiotics and Fermented Foods","field":"Agricultural and Biological Sciences","cited_by":23,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan; Saskatchewan Disease Control Laboratory; Manitoba Health; University of Manitoba; Public Health Agency of Canada","funders":"","keywords":"Metagenomics; Subtyping; Multiplex; Biology; Shigella; Salmonella; Campylobacter; Microbiome; Microbiological culture; Pathogen; Multiplex polymerase chain reaction; Gold standard (test); Microbiology; Polymerase chain reaction; Computational biology; Medicine; Bioinformatics; Genetics; Bacteria; Gene","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":[0.008264662,0.00119436,0.001768733,0.00537358,0.0004755208,0.002775486,0.0009934708,0.001289148,0.003801094],"category_scores_gemma":[0.010592,0.000725108,0.00121798,0.004571195,0.0006898738,0.001876084,0.002380427,0.001591247,0.001488764],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001011842,"about_ca_system_score_gemma":0.001210255,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002154279,"about_ca_topic_score_gemma":0.004722839,"domain_scores_codex":[0.9914973,0.003075938,0.0004999461,0.001360308,0.003264106,0.0003023283],"domain_scores_gemma":[0.9924299,0.001769856,0.001805308,0.0009463876,0.002573417,0.0004751183],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001705443,0.0004505716,0.424171,0.002604433,0.002152215,0.0006012075,0.0009708019,0.004832119,0.2299564,0.003209351,0.01285142,0.316495],"study_design_scores_gemma":[0.0002600479,0.002515464,0.5420178,0.001754089,0.001499131,0.004515143,0.002440615,0.03020741,0.1938502,0.01328389,0.207196,0.0004602982],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6271112,0.06044248,0.2346061,0.01942552,0.001355377,0.000975973,0.02679058,0.004496619,0.02479616],"genre_scores_gemma":[0.736865,0.01923636,0.2179405,0.003820407,0.0005851017,0.0005720407,0.01458409,0.0007144716,0.005681987],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.008264662,"threshold_uncertainty_score":0.04370821,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02256993602124431,"score_gpt":0.2415921977907503,"score_spread":0.219022261769506,"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."}}