{"id":"https://openalex.org/W7212371058","doi":"https://doi.org/10.64898/2026.09.10.26362730","title":"Ruling resistance out, and reading the blank: genome-based antimicrobial susceptibility prediction in clinical Pseudomonas aeruginosa isolates","display_name":"Ruling resistance out, and reading the blank: genome-based antimicrobial susceptibility prediction in clinical Pseudomonas aeruginosa isolates","publication_year":2026,"publication_date":"2026-09-11","ids":{"openalex":"https://openalex.org/W7212371058","doi":"https://doi.org/10.64898/2026.09.10.26362730"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.10.26362730","doi":"https://doi.org/10.64898/2026.09.10.26362730","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.26362730","pdf_url":"https://www.medrxiv.org/content/medrxiv/early/2026/09/11/2026.09.10.26362730.full.pdf","source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"medRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.medrxiv.org/content/medrxiv/early/2026/09/11/2026.09.10.26362730.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5151538669","display_name":"Linda Scheper","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"L. Scheper","raw_affiliation_strings":["Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany","institution_ids":["https://openalex.org/I4210124929"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023530213","display_name":"Jelena Erdmann","orcid":"https://orcid.org/0000-0001-6928-3326","observed_orcids":["https://orcid.org/0000-0001-6928-3326"]},"institutions":[{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]},{"id":"https://openalex.org/I4210151865","display_name":"Center for Experimental and Clinical Infection Research","ror":"https://ror.org/04bya8j72","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I34809795","https://openalex.org/I4210124929","https://openalex.org/I4210151865"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"J. Erdmann","raw_affiliation_strings":["Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany","Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany","institution_ids":["https://openalex.org/I4210124929"]},{"raw_affiliation_string":"Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany","institution_ids":["https://openalex.org/I4210151865"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091002552","display_name":"Ann Kathrin Heroven","orcid":"https://orcid.org/0000-0002-2040-1747","observed_orcids":["https://orcid.org/0000-0002-2040-1747"]},"institutions":[{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"A. K. Heroven","raw_affiliation_strings":["Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany","institution_ids":["https://openalex.org/I4210124929"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021794796","display_name":"Leonard Knegendorf","orcid":"https://orcid.org/0000-0001-8469-1248","observed_orcids":["https://orcid.org/0000-0001-8469-1248"]},"institutions":[{"id":"https://openalex.org/I34809795","display_name":"Medizinische Hochschule Hannover","ror":"https://ror.org/00f2yqf98","country_code":"DE","type":"education","lineage":["https://openalex.org/I34809795"]},{"id":"https://openalex.org/I4210151865","display_name":"Center for Experimental and Clinical Infection Research","ror":"https://ror.org/04bya8j72","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I34809795","https://openalex.org/I4210124929","https://openalex.org/I4210151865"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"L. Knegendorf","raw_affiliation_strings":["Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany","Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany","institution_ids":["https://openalex.org/I34809795"]},{"raw_affiliation_string":"Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany","institution_ids":["https://openalex.org/I4210151865"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008967334","display_name":"Karen Leth Nielsen","orcid":"https://orcid.org/0000-0002-7912-1985","observed_orcids":["https://orcid.org/0000-0002-7912-1985"]},"institutions":[{"id":"https://openalex.org/I2802567020","display_name":"Copenhagen University Hospital","ror":"https://ror.org/05bpbnx46","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020"]},{"id":"https://openalex.org/I2802709434","display_name":"Rigshospitalet","ror":"https://ror.org/03mchdq19","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020","https://openalex.org/I2802709434","https://openalex.org/I4210145385"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"K. Nielsen Leith","raw_affiliation_strings":["Department of Clinical Microbiology, Copenhagen University Hospital \u2013 Rigshospitalet, Copenhagen, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Microbiology, Copenhagen University Hospital \u2013 Rigshospitalet, Copenhagen, Denmark","institution_ids":["https://openalex.org/I2802567020","https://openalex.org/I2802709434"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020495487","display_name":"Frederik Bo\u00ebtius Hertz","orcid":"https://orcid.org/0000-0003-0888-4616","observed_orcids":["https://orcid.org/0000-0003-0888-4616"]},"institutions":[{"id":"https://openalex.org/I2802567020","display_name":"Copenhagen University Hospital","ror":"https://ror.org/05bpbnx46","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020"]},{"id":"https://openalex.org/I2802709434","display_name":"Rigshospitalet","ror":"https://ror.org/03mchdq19","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020","https://openalex.org/I2802709434","https://openalex.org/I4210145385"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"F. Boetius Hertz","raw_affiliation_strings":["Department of Clinical Microbiology, Copenhagen University Hospital \u2013 Rigshospitalet, Copenhagen, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Microbiology, Copenhagen University Hospital \u2013 Rigshospitalet, Copenhagen, Denmark","institution_ids":["https://openalex.org/I2802567020","https://openalex.org/I2802709434"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5122942019","display_name":"Susanne H\u00e4ussler","orcid":"https://orcid.org/0000-0001-6141-9102","observed_orcids":["https://orcid.org/0000-0001-6141-9102"]},"institutions":[{"id":"https://openalex.org/I34809795","display_name":"Medizinische Hochschule Hannover","ror":"https://ror.org/00f2yqf98","country_code":"DE","type":"education","lineage":["https://openalex.org/I34809795"]},{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]},{"id":"https://openalex.org/I4210151865","display_name":"Center for Experimental and Clinical Infection Research","ror":"https://ror.org/04bya8j72","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I34809795","https://openalex.org/I4210124929","https://openalex.org/I4210151865"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"S. H\u00e4ussler","raw_affiliation_strings":["Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany","Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany","Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany","Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany","institution_ids":["https://openalex.org/I34809795"]},{"raw_affiliation_string":"Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany","institution_ids":["https://openalex.org/I4210124929"]},{"raw_affiliation_string":"Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany","institution_ids":["https://openalex.org/I34809795"]},{"raw_affiliation_string":"Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany","institution_ids":["https://openalex.org/I4210151865"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9740999937057495,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9740999937057495,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.011500000022351742,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10195","display_name":"Antimicrobial Resistance in Staphylococcus","score":0.0038999998942017555,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pseudomonas-aeruginosa","display_name":"Pseudomonas aeruginosa","score":0.9110000133514404},{"id":"https://openalex.org/keywords/antimicrobial-susceptibility-prediction","display_name":"antimicrobial susceptibility prediction","score":0.9039999842643738},{"id":"https://openalex.org/keywords/antimicrobial-resistance","display_name":"antimicrobial resistance","score":0.7020000219345093},{"id":"https://openalex.org/keywords/ciprofloxacin-resistance","display_name":"ciprofloxacin resistance","score":0.8870000243186951},{"id":"https://openalex.org/keywords/meropenem-resistance","display_name":"meropenem resistance","score":0.9350000023841858},{"id":"https://openalex.org/keywords/ceftazidime-resistance","display_name":"ceftazidime resistance","score":0.9110000133514404},{"id":"https://openalex.org/keywords/tobramycin-resistance","display_name":"tobramycin resistance","score":0.9860000014305115},{"id":"https://openalex.org/keywords/ampc-beta-lactamase","display_name":"AmpC beta-lactamase","score":0.8989999890327454},{"id":"https://openalex.org/keywords/clinical-breakpoints","display_name":"clinical breakpoints","score":0.5090000033378601},{"id":"https://openalex.org/keywords/resistance-determinants","display_name":"resistance determinants","score":0.414000004529953},{"id":"https://openalex.org/keywords/clinical-isolates","display_name":"clinical isolates","score":0.6269999742507935}],"concepts":[{"id":"https://openalex.org/C2777637488","wikidata":"https://www.wikidata.org/wiki/Q31856","display_name":"Pseudomonas aeruginosa","level":3,"score":0.8003000020980835},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.663100004196167},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.6111999750137329},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5673999786376953},{"id":"https://openalex.org/C200082930","wikidata":"https://www.wikidata.org/wiki/Q22327148","display_name":"Efflux","level":2,"score":0.5654000043869019},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.5577999949455261},{"id":"https://openalex.org/C2778512257","wikidata":"https://www.wikidata.org/wiki/Q256602","display_name":"Ciprofloxacin","level":3,"score":0.5546000003814697},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.5539000034332275},{"id":"https://openalex.org/C2779375183","wikidata":"https://www.wikidata.org/wiki/Q421670","display_name":"Meropenem","level":4,"score":0.5325999855995178},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.47209998965263367},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4474000036716461},{"id":"https://openalex.org/C114851261","wikidata":"https://www.wikidata.org/wiki/Q12147416","display_name":"Drug resistance","level":2,"score":0.44429999589920044},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4198000133037567},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3944000005722046},{"id":"https://openalex.org/C4937899","wikidata":"https://www.wikidata.org/wiki/Q68541106","display_name":"Antimicrobial","level":2,"score":0.3635999858379364},{"id":"https://openalex.org/C133936738","wikidata":"https://www.wikidata.org/wiki/Q643839","display_name":"Multiple drug resistance","level":3,"score":0.3301999866962433},{"id":"https://openalex.org/C57473165","wikidata":"https://www.wikidata.org/wiki/Q7315604","display_name":"Resistance (ecology)","level":2,"score":0.3264000117778778},{"id":"https://openalex.org/C77434933","wikidata":"https://www.wikidata.org/wiki/Q4043440","display_name":"Multilocus sequence typing","level":4,"score":0.2978000044822693},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.26350000500679016},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.25690001249313354},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.2515000104904175}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.10.26362730","doi":"https://doi.org/10.64898/2026.09.10.26362730","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.26362730","pdf_url":"https://www.medrxiv.org/content/medrxiv/early/2026/09/11/2026.09.10.26362730.full.pdf","source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"medRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.10.26362730","doi":"https://doi.org/10.64898/2026.09.10.26362730","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.26362730","pdf_url":"https://www.medrxiv.org/content/medrxiv/early/2026/09/11/2026.09.10.26362730.full.pdf","source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"medRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.9391000270843506,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7212371058.pdf","grobid_xml":"https://content.openalex.org/works/W7212371058.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1582758854","https://openalex.org/W1918156516","https://openalex.org/W2007889243","https://openalex.org/W2018300362","https://openalex.org/W2020018978","https://openalex.org/W2037685605","https://openalex.org/W2095971260","https://openalex.org/W2106359046","https://openalex.org/W2106578604","https://openalex.org/W2106948630","https://openalex.org/W2114297602","https://openalex.org/W2117259850","https://openalex.org/W2119209016","https://openalex.org/W2119910794","https://openalex.org/W2133120177","https://openalex.org/W2133740160","https://openalex.org/W2145918716","https://openalex.org/W2149280174","https://openalex.org/W2167566168","https://openalex.org/W2551267404","https://openalex.org/W2619049102","https://openalex.org/W2769066464","https://openalex.org/W2804230504","https://openalex.org/W2804945403","https://openalex.org/W2891078715","https://openalex.org/W3006176809","https://openalex.org/W3162905453","https://openalex.org/W3170689505","https://openalex.org/W4390431564","https://openalex.org/W4414903417","https://openalex.org/W4417458415","https://openalex.org/W7161242394"],"related_works":["https://openalex.org/W3162905453","https://openalex.org/W3006176809","https://openalex.org/W4308637031","https://openalex.org/W4399440021","https://openalex.org/W2620992520","https://openalex.org/W4224433802","https://openalex.org/W2739559315","https://openalex.org/W3154672499","https://openalex.org/W7223427154","https://openalex.org/W4399523922"],"abstract_inverted_index":{"Abstract":[0],"Genomic":[1,79],"prediction":[2],"of":[3,59,106,110,120,177,188,197,213,217,251,261,270,288,305,313,322,383,402,409],"antimicrobial":[4],"susceptibility":[5,70,178,315],"aims":[6],"to":[7,13,22,172,363,422,427],"identify":[8],"resistance":[9,40,121,149,174,201,221,263],"determinants":[10,119],"and":[11,77,219,237,275,295,417],"thereby":[12],"report":[14],"those":[15,152,269,368],"antibiotics":[16,138,386],"for":[17,73,209,225,235,325,341,381],"which":[18,39,144],"therapeutic":[19],"failure":[20],"is":[21,257,284,344],"be":[23,82,204,223,350,364,394],"expected.":[24],"We":[25],"investigated":[26,387],"what":[27],"this":[28,49,159,329],"approach":[29],"can":[30,349,392],"achieve":[31],"in":[32,38,45,229,334,366],"Pseudomonas":[33],"aeruginosa":[34],",":[35],"a":[36,129,210,230,289,314,335,412],"species":[37],"often":[41],"arises":[42],"through":[43,123],"changes":[44],"gene":[46,111],"expression.":[47,373],"For":[48,308,331,353],"purpose,":[50],"5,749":[51],"consecutive":[52],"clinical":[53,281,429],"isolates":[54,142,242,277,421],"from":[55,151],"the":[56,92,107,140,162,185,194,198,215,252,271,280,285,291,310,319,376,384,397,400,419,428],"routine":[57],"laboratories":[58],"two":[60,253,272,382],"tertiary":[61],"care":[62],"centers":[63],"were":[64,89,179,243],"sequenced,":[65],"each":[66],"with":[67,148,206,370,406],"paired":[68],"phenotypic":[69],"test":[71],"results":[72,348],"ciprofloxacin,":[74],"ceftazidime,":[75,354],"meropenem,":[76,309],"tobramycin.":[78],"variation":[80],"could":[81,202,222],"interpreted":[83],"only":[84,203],"after":[85],"three":[86],"adaptations.":[87],"Variants":[88],"called":[90],"against":[91,98],"population-wide":[93],"major":[94],"allele":[95],"rather":[96,165,246],"than":[97,166,247],"PAO1.":[99],"This":[100],"removes":[101],"markers":[102,146,176,361],"that":[103,153,192,359],"are":[104],"artefacts":[105],"reference.":[108],"Loss":[109],"function":[112],"was":[113],"captured":[114],"systematically,":[115],"as":[116,184,297,302,415],"many":[117],"genetic":[118],"act":[122],"loss-of-function":[124],"mechanisms.":[125],"Furthermore,":[126],"we":[127],"introduced":[128],"specificity":[130],"ratio":[131],"\u2014":[132,143],"enabled":[133],"by":[134,355],"testing":[135],"all":[136],"four":[137,385],"on":[139],"same":[141],"separated":[145],"associated":[147,369],"mechanisms":[150],"merely":[154],"tracked":[155],"clonal":[156],"lineage;":[157],"without":[158],"distinction,":[160],"expanding":[161],"catalogue":[163],"reduced":[164],"improved":[167],"predictive":[168],"performance.":[169],"In":[170],"addition":[171],"classical":[173],"determinants,":[175],"taken":[180],"into":[181,249],"account,":[182],"such":[183],"functional":[186],"loss":[187],"an":[189,259,303,403,423],"efflux":[190],"pump":[191],"exports":[193],"antibiotic":[195],"out":[196],"cell.":[199],"While":[200],"assigned":[205],"corresponding":[207],"confidence":[208],"few":[211],"percent":[212],"isolates,":[214,228,343],"absence":[216,260],"ciprofloxacin":[218,326],"meropenem":[220],"reported":[224,273],"substantially":[226],"more":[227],"conservative":[231],"deduplicated":[232],"analysis":[233],"even":[234],"43%":[236],"87%,":[238],"respectively.":[239],"The":[240,255],"remaining":[241,420],"left":[244],"blank":[245,256],"forced":[248],"one":[250],"categories.":[254],"not":[258],"information:":[262],"rates":[264],"within":[265],"it":[266,327,357],"lay":[267],"between":[268],"groups,":[274],"its":[276],"clustered":[278],"around":[279],"breakpoint.":[282,430],"It":[283],"genomic":[286],"counterpart":[287],"population":[290],"phenotype":[292],"already":[293,317,393],"recognizes":[294],"reports":[296],"susceptible,":[298],"increased":[299,371],"exposure":[300],"or":[301],"area":[304],"technical":[306],"uncertainty.":[307],"residual":[311],"risk":[312],"finding":[316],"meets":[318],"accepted":[320],"threshold":[321],"3%,":[323],"while":[324],"approaches":[328],"threshold.":[330],"tobramycin,":[332],"validation":[333],"larger":[336],"cohort,":[337],"possibly":[338],"specifically":[339],"enriched":[340],"resistant":[342],"required":[345],"before":[346],"our":[347],"considered":[351],"reliable.":[352],"contrast,":[356],"appears":[358],"additional":[360],"need":[362],"identified,":[365],"particular":[367],"AmpC":[372],"Taken":[374],"together,":[375],"present":[377],"data":[378],"show":[379],"that,":[380],"here,":[388],"clinically":[389],"relevant":[390],"findings":[391],"generated":[395],"today:":[396],"genome":[398],"allows":[399],"identification":[401],"isolate":[404],"group":[405,414],"no":[407],"indication":[408],"resistance,":[410],"marks":[411],"smaller":[413],"resistant,":[416],"assigns":[418],"intermediate":[424],"range":[425],"close":[426]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-13T00:00:00"}
