{ "abstract": "SCOPE: The 2017 European Committee on Antimicrobial Susceptibility Testing (EUCAST) subcommittee report on the role of whole genome sequencing (WGS) in antimicrobial susceptibility testing (AST) concluded that WGS antimicrobial susceptibility prediction (WGS-ASP) was not a sufficiently robust alternative to AST to guide clinical decision making at that stage and that more evidence was required [1]. Since then, the use of WGS, bioinformatic tools, machine learning (ML)/artificial intelligence (AI), databases, and prediction approaches has greatly expanded, along with an increased knowledge of resistance mechanisms and their contribution to antimicrobial susceptibility. In response, a new EUCAST ad hoc subcommittee was established in 2024 to review the literature, with the aim of assessing the current potential and limitations of WGS-ASP. METHODS: As in the previous report, the subcommittee reviewed the literature on a 'by organism' basis but expanded the list to also include enterococci, Haemophilus influenzae, and Bacteroides fragilis in addition to those already included in the first version: Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii, Neisseria gonorrhoeae, Staphylococcus aureus, Streptococcus pneumoniae, Clostridioides difficile, and Mycobacterium tuberculosis. Additional sections were included to cover advances in metagenomics, other omics technologies and ML/AI. The full report was compiled and reviewed by all subcommittee members before public consultation in November 2025. CONCLUSIONS AND RECOMMENDATIONS: Significant progress has been achieved in WGS-ASP, with growing evidence supporting its ability to distinguish wild-type from non-wild-type isolates and, consequently, susceptible from resistant strains, particularly for M. tuberculosis and when clinical breakpoints align with the epidemiological cut-off (ECOFF). Despite these advances, important challenges remain before WGS-ASP can be adopted as a clinical decision-making tool. Addressing these gaps will require integrated phenotypic and genotypic surveillance to strengthen the evidence base for complex resistance mechanisms and newer antimicrobial agents, alongside comparative assessments that consider both ECOFF and clinical breakpoints. The analyses will require reference method phenotypic AST and high-quality genomic data. It is critical to ensure that datasets reflect the target populations and encompass the full spectrum of antimicrobial susceptibility, while developing unified interpretation frameworks and harmonized bioinformatics tools to standardize outputs. Robust external quality assessment schemes will be essential for clinical validation, and emerging technologies such as AI and ML offer promising avenues to enhance predictive accuracy. Finally, improvements in cost and turnaround time, coupled with evaluations of setting-specific cost-effectiveness, will be key to enabling practical implementation of WGS-ASP.", "abstract_shown": true, "affiliations": [ "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", "Servicio de Microbiología, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain", "Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark", "Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark", "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", "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", "Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland", "Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA", "Institute of Medical Microbiology and Virology, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany", "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", "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", "Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit. 2, AMR & HCAI Division, UK Health Security Agency, London, UK", "Laboratoire Chrono-environnement (UMR 6249), University Marie and Louis Pasteur, Laboratoire de bactériologie CHU Besançon, CNRS, Besançon, France", "EUCAST Development Laboratory, Central Hospital, Växjö, Sweden", "Department of Genetics, University of Cambridge, Cambridge, UK; Department of Biomedical and Clinical Sciences, Division of Infection and Inflammation, Linköping University, Linköping, Sweden", "Division of Infectious Diseases and Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA", "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", "Laboratory of Clinical Microbiology, Attikon University Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece", "Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME and AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Bactériologie, Paris, France", "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", "Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia", "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", "M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada", "Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden", "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" ], "article_type": "review", "arxiv": null, "author_total": 27, "authors": [ { "affs": [ 0 ], "name": "Ørjan Samuelsen", "orcid": "0000-0002-5525-2614" }, { "affs": [ 1 ], "name": "Carla López-Causapé", "orcid": "0000-0003-2228-2005" }, { "affs": [ 2 ], "name": "Frank M. Aarestrup", "orcid": "0000-0002-7116-2723" }, { "affs": [ 3 ], "name": "Valeria Bortolaia", "orcid": "0000-0001-6559-7344" }, { "affs": [ 4 ], "name": "Michael S. M. Brouwer", "orcid": "0000-0002-1067-7555" }, { "affs": [ 5 ], "name": "Rafael Cantón", "orcid": "0000-0003-1675-3173" }, { "affs": [ 6 ], "name": "Adrian Egli", "orcid": "0000-0002-3564-8603" }, { "affs": [ 7 ], "name": "Yonatan H. Grad", "orcid": "0000-0001-5646-1314" }, { "affs": [ 8 ], "name": "Axel G. Hamprecht", "orcid": "0000-0003-1449-5780" }, { "affs": [ 9 ], "name": "Susanne Häußler", "orcid": "0000-0001-6141-9102" }, { "affs": [ 10 ], "name": "Kathryn E. Holt", "orcid": "0000-0003-3949-2471" }, { "affs": [ 11 ], "name": "Katie L. Hopkins", "orcid": "0000-0001-7279-5322" }, { "name": "Benjamin P. Howden", "orcid": "0000-0003-0237-1473" }, { "affs": [ 12 ], "name": "Katy Jeannot", "orcid": "0000-0002-4634-8550" }, { "affs": [ 13 ], "name": "Gunnar Kahlmeter", "orcid": "0000-0001-9993-9891" }, { "affs": [ 14 ], "name": "Claudio Umberto Köser", "orcid": "0000-0002-0232-846X" }, { "affs": [ 15 ], "name": "Amy J. Mathers", "orcid": "0000-0002-3533-6351" }, { "affs": [ 16 ], "name": "Thierry Naas", "orcid": "0000-0001-9937-9572" }, { "affs": [ 17 ], "name": "Spyros Pournaras", "orcid": "0000-0002-6298-9577" }, { "affs": [ 18 ], "name": "Étienne Ruppé", "orcid": "0000-0002-1178-0298" }, { "affs": [ 19 ], "name": "Thomas Schön", "orcid": "0000-0003-4849-1286" }, { "name": "Nicole Stoesser", "orcid": "0000-0002-4508-7969" }, { "affs": [ 20 ], "name": "John D. Turnidge", "orcid": "0000-0003-4240-5578" }, { "affs": [ 21 ], "name": "Guido Werner" }, { "affs": [ 22 ], "name": "Gerard D. Wright", "orcid": "0000-0002-9129-7131" }, { "affs": [ 23 ], "name": "Christian G. Giske", "orcid": "0000-0003-4327-6122" }, { "affs": [ 24 ], "name": "Antonio Oliver", "orcid": "0000-0001-9327-1894" } ], "bibtex": "https://research.draconitic.com/paper/ageyx7p2ke701.bib", "cited_by": 17, "doi": "10.1016/j.cmi.2026.05.012", "fulltext_url": null, "id": "ageyx7p2ke701", "issns": [ "1198-743X", "1469-0691" ], "landing_url": "https://doi.org/10.1016/j.cmi.2026.05.012", "language": "en", "licence": "CC-BY-NC-ND", "licence_label": "CC BY-NC-ND", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1308|Bacterial Identification and Susceptibility Testing" ], [ "openalex", "2726|Bacterial Identification and Susceptibility Testing" ] ], "openalex": "W7161242394", "pdf_url": null, "pmcid": null, "pmid": "42142806", "published": "2026-05-16", "publisher": "Elsevier BV", "ris": "https://research.draconitic.com/paper/ageyx7p2ke701.ris", "sources": [ { "first_seen": "2026-11-05T13:20:46Z", "native_id": "W7161242394", "source": "openalex", "url": "https://doi.org/10.1016/j.cmi.2026.05.012" } ], "subjects": [ { "field": "medicine", "origin": "openalex:2726|Bacterial Identification and Susceptibility Testing", "subfield": "infectious-disease" } ], "title": "The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the European Committee on Antimicrobial Susceptibility Testing Subcommittee", "title_text": "The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the European Committee on Antimicrobial Susceptibility Testing Subcommittee", "type": "peer-reviewed", "updated_at": "2026-11-09T13:21:15Z", "url": "https://research.draconitic.com/paper/ageyx7p2ke701", "venue": "Clinical Microbiology and Infection", "versions": [] }