{"id":"W4416011990","doi":"10.1101/2025.11.06.25339637","title":"Using Genomic and Traditional Epidemiologic Approaches to Define Complex Transmission Pathways of <i>Klebsiella pneumoniae</i> Infection in a Neonatal Unit in Botswana, 2022–2023","year":2025,"lang":"","type":"preprint","venue":"medRxiv","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; Hospital for Sick Children","funders":"Centers for Disease Control and Prevention; Bill and Melinda Gates Foundation","keywords":"Outbreak; Multilocus sequence typing; Colonization; Transmission (telecommunications); Typing; Whole genome sequencing; Infection control; Bloodstream infection","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":[0.0007198252,0.0004593416,0.0001802712,0.001704366,0.0005332029,0.0007502993,0.0004102798,0.0003745109,0.0006520974],"category_scores_gemma":[0.002001641,0.0002886775,0.000324606,0.002000906,0.0004460793,0.0003509856,0.0007772846,0.0003114431,0.0001171477],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002105165,"about_ca_system_score_gemma":0.00157315,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0967639,"about_ca_topic_score_gemma":0.1338394,"domain_scores_codex":[0.999651,0.0000930997,0.00004092867,0.00008549276,0.00003436362,0.00009529488],"domain_scores_gemma":[0.9991052,0.0001860029,0.0003522529,0.00005810479,0.000215603,0.00008285557],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00007015026,0.00002303909,0.9878406,0.00004520701,0.00002779561,0.0004002967,0.0007085343,0.0003933279,0.004529248,0.00008959801,0.0000788119,0.005793418],"study_design_scores_gemma":[0.000005441621,0.00006929709,0.9938741,0.00005445709,0.00002689181,0.0005102515,0.002000358,0.002257265,0.0006487121,0.0001243682,0.0004219865,0.000006810101],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9980785,0.0001572421,0.0008080248,0.00009198008,0.000002989374,0.0000271212,0.000388379,0.000006743523,0.0004391813],"genre_scores_gemma":[0.9968635,0.000137164,0.002413157,0.00006492543,0.000002240851,0.00002944565,0.000382132,0.000002383152,0.0001051876],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0967639,"threshold_uncertainty_score":0.1924013,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.204037984518371,"score_gpt":0.2934493436775258,"score_spread":0.08941135915915477,"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."}}