{"id":"W4416297581","doi":"10.1128/spectrum.01768-25","title":"Carbapenem-resistant <i>Acinetobacter baumannii</i> at a hospital in Botswana: detecting a protracted outbreak using whole genome sequencing","year":2025,"lang":"en","type":"article","venue":"Microbiology Spectrum","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hospital for Sick Children; University of Toronto; University of British Columbia","funders":"","keywords":"Outbreak; Whole genome sequencing; DNA sequencing; Genome; Genomics; Transmission (telecommunications); Genomic sequencing; Antibiotic resistance","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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002784138,0.0003979882,0.0004612071,0.0001901215,0.0002018985,0.00004808198,0.0003832915,0.0004514446,0.0000353283],"category_scores_gemma":[0.00008326379,0.0004016281,0.0001506064,0.0003020776,0.000236864,0.00001145433,0.0004221426,0.0002920384,0.00002231664],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005734524,"about_ca_system_score_gemma":0.0002691526,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002574695,"about_ca_topic_score_gemma":0.002298345,"domain_scores_codex":[0.9974707,0.0001550775,0.0005895297,0.0009087372,0.00005217012,0.0008237703],"domain_scores_gemma":[0.9990289,0.00002224352,0.0002207323,0.0006042776,0.00005785554,0.00006595496],"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":[0.0002454953,0.00005125452,0.03817434,0.00004590581,0.00009904384,0.00004788168,0.00005532269,0.00005170212,0.9610531,0.00002153164,0.0001226084,0.00003183002],"study_design_scores_gemma":[0.00189866,0.0004127886,0.07550694,0.0002069896,0.00007373778,0.0001515243,0.0004526514,0.00006698454,0.8959219,0.00006267873,0.02436567,0.0008794405],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9962962,0.0007812805,0.0002975125,0.0003609034,0.0002964048,0.0006713108,0.000103146,0.00003920047,0.001154033],"genre_scores_gemma":[0.9967636,0.00002485232,0.00100514,0.0003882548,0.0001493719,0.00001946448,0.0002840596,0.0000462968,0.001318896],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06513116,"threshold_uncertainty_score":0.9998435,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007075794501044229,"score_gpt":0.2288217196223758,"score_spread":0.2217459251213316,"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."}}