{"id":"W4408803303","doi":"10.1101/2025.03.21.644136","title":"Whole-Genome Sequencing, Annotation and Phenotypic Taxonomic Confirmation of a Multidrug-Resistant <i>Escherichia coli</i> Strain Isolated from the Blood of a Sepsis Patient","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"Invest Northern Ireland","keywords":"Sepsis; Escherichia coli; Whole genome sequencing; Annotation; Multiple drug resistance; Genome; Biology; DNA sequencing; Computational biology; Genetics; Microbiology; Gene; Immunology; Drug 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004273262,0.0006012288,0.0007208611,0.0009294151,0.0004640308,0.0009636314,0.0003419986,0.0008298323,0.0007621527],"category_scores_gemma":[0.0009649364,0.0002286536,0.001098583,0.001510528,0.0002972188,0.0002945471,0.0005494069,0.000787281,0.0008308942],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002243697,"about_ca_system_score_gemma":0.0006808962,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002966274,"about_ca_topic_score_gemma":0.002466995,"domain_scores_codex":[0.9993572,0.00007430643,0.00008285031,0.00019224,0.0001908473,0.0001026527],"domain_scores_gemma":[0.9994158,0.0001160341,0.0001452377,0.00006111006,0.0001808593,0.00008101916],"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":[0.0005442135,0.0002099076,0.01784192,0.0006006443,0.00009508024,0.002037943,0.0005270745,0.0005324195,0.9589034,0.0001394946,0.001055129,0.01751267],"study_design_scores_gemma":[0.0001078417,0.001522157,0.5943465,0.0004080816,0.000853497,0.01239489,0.00306968,0.008423713,0.329962,0.0004917918,0.0482233,0.0001966112],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9636026,0.002019761,0.006688538,0.0006427417,0.0001464861,0.0002019673,0.02457047,0.0002948657,0.001832611],"genre_scores_gemma":[0.9122263,0.001825413,0.03021658,0.00056597,0.00008723861,0.0001301202,0.05276964,0.000250681,0.001928063],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002966274,"threshold_uncertainty_score":0.005898058,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009265972972393708,"score_gpt":0.2039968143331843,"score_spread":0.1947308413607906,"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."}}