The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the European Committee on Antimicrobial Susceptibility Testing Subcommittee.
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| Title: | The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the European Committee on Antimicrobial Susceptibility Testing Subcommittee. |
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| Authors: | Samuelsen Ø; Norwegian Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway. Electronic address: orjan.samuelsen@unn.no., López-Causapé C; Servicio de Microbiología, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain., Aarestrup FM; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark., Bortolaia V; Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark., Brouwer MSM; Wageningen Bioveterinary Research, Part of Wageningen University and Research, Lelystad, The Netherlands; Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands., Cantón R; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain., Egli A; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland., Grad YH; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA., Hamprecht A; Institute of Medical Microbiology and Virology, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany., Haussler S; Department of Molecular Bacteriology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany; Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture of the Hannover Medical School (MHH) and the HZI, Hannover, Germany; Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark., Holt KE; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria, Australia., Hopkins KL; Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit. 2, AMR & HCAI Division, UK Health Security Agency, London, UK., Howden BP; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Melbourne, Victoria, Australia., Jeannot K; Laboratoire Chrono-environnement (UMR 6249), University Marie and Louis Pasteur, Laboratoire de bactériologie CHU Besançon, CNRS, Besançon, France., Kahlmeter G; EUCAST Development Laboratory, Central Hospital, Växjö, Sweden., Köser CU; Department of Genetics, University of Cambridge, Cambridge, UK; Department of Biomedical and Clinical Sciences, Division of Infection and Inflammation, Linköping University, Linköping, Sweden., Mathers AJ; Division of Infectious Diseases and Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA., Naas T; Team 'Resist', UMR1184, INSERM, Faculty of Medicine, Université Paris-Saclay, CEA, Le Kremlin-Bicêtre, France; Department of Bacteriology-Hygiene, Bicêtre Hospital, AP-HP Paris-Saclay, Le Kremlin-Bicêtre, France; French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacterales, Le Kremlin-Bicêtre, France., Pournaras S; Laboratory of Clinical Microbiology, Attikon University Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece., Ruppé E; Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME and AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Bactériologie, Paris, France., Schön T; Department of Biomedical and Clinical Sciences, Division of Infection and Inflammation, Linköping University, Linköping, Sweden; Department of Infectious Diseases, Kalmar County Hospital, Linköping University, Kalmar, Sweden; Department of Infectious Diseases, Linköping University Hospital, Linköping, Sweden., Stoesser N; Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with UK Health Security Agency, Nuffield Department of Medicine, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK., Turnidge J; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia., Werner G; Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany; National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany., Wright GD; M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada., Giske CG; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden., Oliver A; Servicio de Microbiología, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain. Electronic address: antonio.oliver@ssib.es. |
| Source: | Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases [Clin Microbiol Infect] 2026 Jun; Vol. 32 (7S), pp. S1-S34. Date of Electronic Publication: 2026 May 15. |
| Publication Type: | Journal Article; Review |
| Journal Info: | Publisher: Elsevier Country of Publication: England NLM ID: 9516420 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1469-0691 (Electronic) Linking ISSN: 1198743X NLM ISO Abbreviation: Clin Microbiol Infect Subsets: MEDLINE |
| Database: | MEDLINE Ultimate |
| FullText | Text: Availability: 0 |
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| Header | DbId: mdl DbLabel: MEDLINE Ultimate An: 42142806 AccessLevel: 2 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the European Committee on Antimicrobial Susceptibility Testing Subcommittee. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AU" term="%22Samuelsen+Ø%22">Samuelsen Ø</searchLink>; Norwegian Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway. Electronic address: orjan.samuelsen@unn.no.<br /><searchLink fieldCode="AU" term="%22López-Causapé+C%22">López-Causapé C</searchLink>; Servicio de Microbiología, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.<br /><searchLink fieldCode="AU" term="%22Aarestrup+FM%22">Aarestrup FM</searchLink>; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark.<br /><searchLink fieldCode="AU" term="%22Bortolaia+V%22">Bortolaia V</searchLink>; Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.<br /><searchLink fieldCode="AU" term="%22Brouwer+MSM%22">Brouwer MSM</searchLink>; Wageningen Bioveterinary Research, Part of Wageningen University and Research, Lelystad, The Netherlands; Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.<br /><searchLink fieldCode="AU" term="%22Cantón+R%22">Cantón R</searchLink>; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.<br /><searchLink fieldCode="AU" term="%22Egli+A%22">Egli A</searchLink>; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.<br /><searchLink fieldCode="AU" term="%22Grad+YH%22">Grad YH</searchLink>; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA.<br /><searchLink fieldCode="AU" term="%22Hamprecht+A%22">Hamprecht A</searchLink>; Institute of Medical Microbiology and Virology, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.<br /><searchLink fieldCode="AU" term="%22Haussler+S%22">Haussler S</searchLink>; Department of Molecular Bacteriology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany; Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture of the Hannover Medical School (MHH) and the HZI, Hannover, Germany; Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.<br /><searchLink fieldCode="AU" term="%22Holt+KE%22">Holt KE</searchLink>; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria, Australia.<br /><searchLink fieldCode="AU" term="%22Hopkins+KL%22">Hopkins KL</searchLink>; Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit. 2, AMR & HCAI Division, UK Health Security Agency, London, UK.<br /><searchLink fieldCode="AU" term="%22Howden+BP%22">Howden BP</searchLink>; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Melbourne, Victoria, Australia.<br /><searchLink fieldCode="AU" term="%22Jeannot+K%22">Jeannot K</searchLink>; Laboratoire Chrono-environnement (UMR 6249), University Marie and Louis Pasteur, Laboratoire de bactériologie CHU Besançon, CNRS, Besançon, France.<br /><searchLink fieldCode="AU" term="%22Kahlmeter+G%22">Kahlmeter G</searchLink>; EUCAST Development Laboratory, Central Hospital, Växjö, Sweden.<br /><searchLink fieldCode="AU" term="%22Köser+CU%22">Köser CU</searchLink>; Department of Genetics, University of Cambridge, Cambridge, UK; Department of Biomedical and Clinical Sciences, Division of Infection and Inflammation, Linköping University, Linköping, Sweden.<br /><searchLink fieldCode="AU" term="%22Mathers+AJ%22">Mathers AJ</searchLink>; Division of Infectious Diseases and Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA.<br /><searchLink fieldCode="AU" term="%22Naas+T%22">Naas T</searchLink>; Team 'Resist', UMR1184, INSERM, Faculty of Medicine, Université Paris-Saclay, CEA, Le Kremlin-Bicêtre, France; Department of Bacteriology-Hygiene, Bicêtre Hospital, AP-HP Paris-Saclay, Le Kremlin-Bicêtre, France; French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacterales, Le Kremlin-Bicêtre, France.<br /><searchLink fieldCode="AU" term="%22Pournaras+S%22">Pournaras S</searchLink>; Laboratory of Clinical Microbiology, Attikon University Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.<br /><searchLink fieldCode="AU" term="%22Ruppé+E%22">Ruppé E</searchLink>; Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME and AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Bactériologie, Paris, France.<br /><searchLink fieldCode="AU" term="%22Schön+T%22">Schön T</searchLink>; Department of Biomedical and Clinical Sciences, Division of Infection and Inflammation, Linköping University, Linköping, Sweden; Department of Infectious Diseases, Kalmar County Hospital, Linköping University, Kalmar, Sweden; Department of Infectious Diseases, Linköping University Hospital, Linköping, Sweden.<br /><searchLink fieldCode="AU" term="%22Stoesser+N%22">Stoesser N</searchLink>; Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with UK Health Security Agency, Nuffield Department of Medicine, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.<br /><searchLink fieldCode="AU" term="%22Turnidge+J%22">Turnidge J</searchLink>; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.<br /><searchLink fieldCode="AU" term="%22Werner+G%22">Werner G</searchLink>; Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany; National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany.<br /><searchLink fieldCode="AU" term="%22Wright+GD%22">Wright GD</searchLink>; M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.<br /><searchLink fieldCode="AU" term="%22Giske+CG%22">Giske CG</searchLink>; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.<br /><searchLink fieldCode="AU" term="%22Oliver+A%22">Oliver A</searchLink>; Servicio de Microbiología, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain. Electronic address: antonio.oliver@ssib.es. – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%229516420%22">Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases</searchLink> [Clin Microbiol Infect] 2026 Jun; Vol. 32 (7S), pp. S1-S34. <i>Date of Electronic Publication: </i>2026 May 15. – Name: TypePub Label: Publication Type Group: TypPub Data: Journal Article; Review – Name: TitleSource Label: Journal Info Group: Src Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Elsevier%22">Elsevier </searchLink><i>Country of Publication: </i>England <i>NLM ID: </i>9516420 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1469-0691 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%221198743X%22">1198743X </searchLink><i>NLM ISO Abbreviation: </i>Clin Microbiol Infect <i>Subsets: </i>MEDLINE |
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