{"id":"W4407667915","doi":"10.1007/s00248-025-02502-7","title":"Quinolone Resistance Genes qnr, aac(6′)-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics","year":2025,"lang":"en","type":"article","venue":"Microbial Ecology","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Japan Society for the Promotion of Science; Kurita Water and Environment Foundation; Environmental Restoration and Conservation Agency","keywords":"Biology; Plasmid; Replicon; Escherichia coli; Genetics; Genome; Circular bacterial chromosome; Quinolone; Microbiology; Comparative genomics; Gene; Antibiotic resistance; Mobile genetic elements; Genomics; Bacteria; Antibiotics","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.00006773101,0.0003081184,0.0004781238,0.00007932251,0.0001342233,0.00003513849,0.0003035404,0.0003830518,0.00003753789],"category_scores_gemma":[0.00001980855,0.0003188641,0.00006356127,0.00008954285,0.0005644833,0.000007482756,0.0003061878,0.0001662582,0.00001886333],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001419563,"about_ca_system_score_gemma":0.0001436621,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001312989,"about_ca_topic_score_gemma":0.01114073,"domain_scores_codex":[0.9982278,0.0002202181,0.000446114,0.0007033021,0.00004402351,0.0003585139],"domain_scores_gemma":[0.9993149,0.00005549275,0.0001531578,0.0003884359,0.00002434685,0.00006368607],"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":[0.0004942295,0.0001308334,0.02668301,0.00001927496,0.0001168396,0.00001443917,0.0005410895,0.00002204213,0.9706404,0.000063611,0.0008940104,0.0003802253],"study_design_scores_gemma":[0.00187998,0.0001699892,0.4548244,0.00003495249,0.00003335792,0.000003630312,0.000399676,0.00004171382,0.4675241,0.0005839624,0.07409749,0.0004067853],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9891015,0.009314645,0.0002104222,0.0001646727,0.0004139777,0.0004377421,0.00007912518,0.00001070484,0.0002672268],"genre_scores_gemma":[0.9936438,0.002015634,0.002702581,0.0006098731,0.0001137778,0.00001933376,0.000197534,0.00002319479,0.0006743029],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5031164,"threshold_uncertainty_score":0.9999263,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005232875358803179,"score_gpt":0.2140643176134716,"score_spread":0.2088314422546684,"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."}}