{"id":"W4411276300","doi":"10.1128/aac.00107-25","title":"Proteogenomic analysis demonstrates increased <i>bla</i> <sub>OXA-48</sub> copy numbers and OmpK36 loss as contributors to carbapenem resistance in <i>Klebsiella pneumoniae</i>","year":2025,"lang":"en","type":"article","venue":"Antimicrobial Agents and Chemotherapy","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"Eurostars; European Commission; Rijksdienst voor Ondernemend Nederland","keywords":"Klebsiella pneumoniae; Klebsiella infections; Biology; Microbiology; Klebsiella; Enterobacteriaceae; Virology; Carbapenem; Genetics; Antibiotics; Escherichia coli; 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":[0.0001052699,0.0003734768,0.0002488958,0.0003622308,0.0001770062,0.0003228053,0.000140422,0.0002686529,0.0006872843],"category_scores_gemma":[0.0002144712,0.0001812452,0.0003477361,0.0003147982,0.0001931181,0.0001569752,0.0002213172,0.0002460822,0.0002608951],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001667017,"about_ca_system_score_gemma":0.0001473045,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001652852,"about_ca_topic_score_gemma":0.001263326,"domain_scores_codex":[0.9997929,0.00002042126,0.00002594332,0.00005609842,0.00005852844,0.00004606251],"domain_scores_gemma":[0.9998378,0.00001764488,0.00006262333,0.00001697478,0.00003064515,0.00003435081],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001105923,0.00001762715,0.00501857,0.00002214943,0.000012716,0.0001182977,0.00003131146,0.00004437229,0.9937487,0.000009199154,0.00002750491,0.0008390048],"study_design_scores_gemma":[0.000009204968,0.0003444017,0.3385294,0.00001206977,0.0001050673,0.002191785,0.0003033825,0.001572261,0.6553652,0.00005035441,0.001495785,0.00002104456],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9983672,0.0001467388,0.000626464,0.00003292453,0.000003780435,0.000009806384,0.0006081037,0.00002340393,0.0001815184],"genre_scores_gemma":[0.9964572,0.0001428169,0.001560629,0.00003482894,0.000003816718,0.00001018873,0.001301728,0.00001386482,0.0004748864],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001652852,"threshold_uncertainty_score":0.003286421,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.002707424753460548,"score_gpt":0.2272578751237332,"score_spread":0.2245504503702726,"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."}}