The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.
Identifieur interne : 001348 ( PubMed/Corpus ); précédent : 001347; suivant : 001349The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.
Auteurs : M J Ellington ; O. Ekelund ; F M Aarestrup ; R. Canton ; M. Doumith ; C. Giske ; H. Grundman ; H. Hasman ; M T G. Holden ; K L Hopkins ; J. Iredell ; G. Kahlmeter ; C U Köser ; A. Macgowan ; D. Mevius ; M. Mulvey ; T. Naas ; T. Peto ; J-M Rolain ; Samuelsen ; N. WoodfordSource :
- Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases [ 1469-0691 ] ; 2017.
English descriptors
- KwdEn :
- MESH :
- chemical , pharmacology : Anti-Bacterial Agents.
- drug effects : Bacteria.
- genetics : Bacteria.
- methods : Microbial Sensitivity Tests.
- Europe, Genome, Bacterial, Internationality.
Abstract
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.
DOI: 10.1016/j.cmi.2016.11.012
PubMed: 27890457
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Ekelund</name><affiliation><nlm:affiliation>Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Aarestrup, F M" sort="Aarestrup, F M" uniqKey="Aarestrup F" first="F M" last="Aarestrup">F M Aarestrup</name><affiliation><nlm:affiliation>National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.</nlm:affiliation></affiliation></author><author><name sortKey="Canton, R" sort="Canton, R" uniqKey="Canton R" first="R" last="Canton">R. Canton</name><affiliation><nlm:affiliation>Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.</nlm:affiliation></affiliation></author><author><name sortKey="Doumith, M" sort="Doumith, M" uniqKey="Doumith M" first="M" last="Doumith">M. Doumith</name><affiliation><nlm:affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Giske, C" sort="Giske, C" uniqKey="Giske C" first="C" last="Giske">C. Giske</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Grundman, H" sort="Grundman, H" uniqKey="Grundman H" first="H" last="Grundman">H. Grundman</name><affiliation><nlm:affiliation>University Medical Centre Freiburg, Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Hasman, H" sort="Hasman, H" uniqKey="Hasman H" first="H" last="Hasman">H. Hasman</name><affiliation><nlm:affiliation>Statens Serum Institute, Department of Microbiology and Infection Control, Copenhagen, Denmark.</nlm:affiliation></affiliation></author><author><name sortKey="Holden, M T G" sort="Holden, M T G" uniqKey="Holden M" first="M T G" last="Holden">M T G. Holden</name><affiliation><nlm:affiliation>School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Hopkins, K L" sort="Hopkins, K L" uniqKey="Hopkins K" first="K L" last="Hopkins">K L Hopkins</name><affiliation><nlm:affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Iredell, J" sort="Iredell, J" uniqKey="Iredell J" first="J" last="Iredell">J. Iredell</name><affiliation><nlm:affiliation>Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Kahlmeter, G" sort="Kahlmeter, G" uniqKey="Kahlmeter G" first="G" last="Kahlmeter">G. Kahlmeter</name><affiliation><nlm:affiliation>Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Koser, C U" sort="Koser, C U" uniqKey="Koser C" first="C U" last="Köser">C U Köser</name><affiliation><nlm:affiliation>Department of Medicine, University of Cambridge, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Macgowan, A" sort="Macgowan, A" uniqKey="Macgowan A" first="A" last="Macgowan">A. Macgowan</name><affiliation><nlm:affiliation>Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Mevius, D" sort="Mevius, D" uniqKey="Mevius D" first="D" last="Mevius">D. Mevius</name><affiliation><nlm:affiliation>Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Mulvey, M" sort="Mulvey, M" uniqKey="Mulvey M" first="M" last="Mulvey">M. Mulvey</name><affiliation><nlm:affiliation>National Microbiology Laboratory, Winnipeg, Manitoba, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Naas, T" sort="Naas, T" uniqKey="Naas T" first="T" last="Naas">T. Naas</name><affiliation><nlm:affiliation>French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre, France.</nlm:affiliation></affiliation></author><author><name sortKey="Peto, T" sort="Peto, T" uniqKey="Peto T" first="T" last="Peto">T. Peto</name><affiliation><nlm:affiliation>Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Rolain, J M" sort="Rolain, J M" uniqKey="Rolain J" first="J-M" last="Rolain">J-M Rolain</name><affiliation><nlm:affiliation>PU-PH des Disciplines Pharmaceutiques, 1-URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Valorization and Transfer, Aix Marseille Université, Faculté de Médecine et de Pharmacie, Marseille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Samuelsen, " sort="Samuelsen, " uniqKey="Samuelsen " first="" last="Samuelsen"> Samuelsen</name><affiliation><nlm:affiliation>Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø, Norway.</nlm:affiliation></affiliation></author><author><name sortKey="Woodford, N" sort="Woodford, N" uniqKey="Woodford N" first="N" last="Woodford">N. Woodford</name><affiliation><nlm:affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK. Electronic address: neil.woodford@phe.gov.uk.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:27890457</idno><idno type="pmid">27890457</idno><idno type="doi">10.1016/j.cmi.2016.11.012</idno><idno type="wicri:Area/PubMed/Corpus">001348</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001348</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.</title><author><name sortKey="Ellington, M J" sort="Ellington, M J" uniqKey="Ellington M" first="M J" last="Ellington">M J Ellington</name><affiliation><nlm:affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Ekelund, O" sort="Ekelund, O" uniqKey="Ekelund O" first="O" last="Ekelund">O. Ekelund</name><affiliation><nlm:affiliation>Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Aarestrup, F M" sort="Aarestrup, F M" uniqKey="Aarestrup F" first="F M" last="Aarestrup">F M Aarestrup</name><affiliation><nlm:affiliation>National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.</nlm:affiliation></affiliation></author><author><name sortKey="Canton, R" sort="Canton, R" uniqKey="Canton R" first="R" last="Canton">R. Canton</name><affiliation><nlm:affiliation>Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.</nlm:affiliation></affiliation></author><author><name sortKey="Doumith, M" sort="Doumith, M" uniqKey="Doumith M" first="M" last="Doumith">M. Doumith</name><affiliation><nlm:affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Giske, C" sort="Giske, C" uniqKey="Giske C" first="C" last="Giske">C. Giske</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Grundman, H" sort="Grundman, H" uniqKey="Grundman H" first="H" last="Grundman">H. Grundman</name><affiliation><nlm:affiliation>University Medical Centre Freiburg, Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Hasman, H" sort="Hasman, H" uniqKey="Hasman H" first="H" last="Hasman">H. Hasman</name><affiliation><nlm:affiliation>Statens Serum Institute, Department of Microbiology and Infection Control, Copenhagen, Denmark.</nlm:affiliation></affiliation></author><author><name sortKey="Holden, M T G" sort="Holden, M T G" uniqKey="Holden M" first="M T G" last="Holden">M T G. Holden</name><affiliation><nlm:affiliation>School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Hopkins, K L" sort="Hopkins, K L" uniqKey="Hopkins K" first="K L" last="Hopkins">K L Hopkins</name><affiliation><nlm:affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Iredell, J" sort="Iredell, J" uniqKey="Iredell J" first="J" last="Iredell">J. Iredell</name><affiliation><nlm:affiliation>Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Kahlmeter, G" sort="Kahlmeter, G" uniqKey="Kahlmeter G" first="G" last="Kahlmeter">G. Kahlmeter</name><affiliation><nlm:affiliation>Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Koser, C U" sort="Koser, C U" uniqKey="Koser C" first="C U" last="Köser">C U Köser</name><affiliation><nlm:affiliation>Department of Medicine, University of Cambridge, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Macgowan, A" sort="Macgowan, A" uniqKey="Macgowan A" first="A" last="Macgowan">A. Macgowan</name><affiliation><nlm:affiliation>Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Mevius, D" sort="Mevius, D" uniqKey="Mevius D" first="D" last="Mevius">D. Mevius</name><affiliation><nlm:affiliation>Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Mulvey, M" sort="Mulvey, M" uniqKey="Mulvey M" first="M" last="Mulvey">M. Mulvey</name><affiliation><nlm:affiliation>National Microbiology Laboratory, Winnipeg, Manitoba, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Naas, T" sort="Naas, T" uniqKey="Naas T" first="T" last="Naas">T. Naas</name><affiliation><nlm:affiliation>French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre, France.</nlm:affiliation></affiliation></author><author><name sortKey="Peto, T" sort="Peto, T" uniqKey="Peto T" first="T" last="Peto">T. Peto</name><affiliation><nlm:affiliation>Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Rolain, J M" sort="Rolain, J M" uniqKey="Rolain J" first="J-M" last="Rolain">J-M Rolain</name><affiliation><nlm:affiliation>PU-PH des Disciplines Pharmaceutiques, 1-URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Valorization and Transfer, Aix Marseille Université, Faculté de Médecine et de Pharmacie, Marseille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Samuelsen, " sort="Samuelsen, " uniqKey="Samuelsen " first="" last="Samuelsen"> Samuelsen</name><affiliation><nlm:affiliation>Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø, Norway.</nlm:affiliation></affiliation></author><author><name sortKey="Woodford, N" sort="Woodford, N" uniqKey="Woodford N" first="N" last="Woodford">N. Woodford</name><affiliation><nlm:affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK. Electronic address: neil.woodford@phe.gov.uk.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases</title><idno type="eISSN">1469-0691</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Anti-Bacterial Agents (pharmacology)</term><term>Bacteria (drug effects)</term><term>Bacteria (genetics)</term><term>Europe</term><term>Genome, Bacterial</term><term>Internationality</term><term>Microbial Sensitivity Tests (methods)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Anti-Bacterial Agents</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Microbial Sensitivity Tests</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Europe</term><term>Genome, Bacterial</term><term>Internationality</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27890457</PMID><DateCreated><Year>2016</Year><Month>11</Month><Day>28</Day></DateCreated><DateCompleted><Year>2017</Year><Month>02</Month><Day>09</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>09</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-0691</ISSN><JournalIssue CitedMedium="Internet"><Volume>23</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases</Title><ISOAbbreviation>Clin. Microbiol. Infect.</ISOAbbreviation></Journal><ArticleTitle>The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.</ArticleTitle><Pagination><MedlinePgn>2-22</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1198-743X(16)30568-7</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.cmi.2016.11.012</ELocationID><Abstract><AbstractText>Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.</AbstractText><CopyrightInformation>Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ellington</LastName><ForeName>M J</ForeName><Initials>MJ</Initials><AffiliationInfo><Affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ekelund</LastName><ForeName>O</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aarestrup</LastName><ForeName>F M</ForeName><Initials>FM</Initials><AffiliationInfo><Affiliation>National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Canton</LastName><ForeName>R</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Doumith</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giske</LastName><ForeName>C</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grundman</LastName><ForeName>H</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>University Medical Centre Freiburg, Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hasman</LastName><ForeName>H</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Statens Serum Institute, Department of Microbiology and Infection Control, Copenhagen, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Holden</LastName><ForeName>M T G</ForeName><Initials>MT</Initials><AffiliationInfo><Affiliation>School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hopkins</LastName><ForeName>K L</ForeName><Initials>KL</Initials><AffiliationInfo><Affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iredell</LastName><ForeName>J</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kahlmeter</LastName><ForeName>G</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Köser</LastName><ForeName>C U</ForeName><Initials>CU</Initials><AffiliationInfo><Affiliation>Department of Medicine, University of Cambridge, Cambridge, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>MacGowan</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mevius</LastName><ForeName>D</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mulvey</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>National Microbiology Laboratory, Winnipeg, Manitoba, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Naas</LastName><ForeName>T</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peto</LastName><ForeName>T</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rolain</LastName><ForeName>J-M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>PU-PH des Disciplines Pharmaceutiques, 1-URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Valorization and Transfer, Aix Marseille Université, Faculté de Médecine et de Pharmacie, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Samuelsen</LastName><ForeName>Ø</ForeName><Initials>Ø</Initials><AffiliationInfo><Affiliation>Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Woodford</LastName><ForeName>N</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK. Electronic address: neil.woodford@phe.gov.uk.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D016454">Review</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>11</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Clin Microbiol Infect</MedlineTA><NlmUniqueID>9516420</NlmUniqueID><ISSNLinking>1198-743X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000900">Anti-Bacterial Agents</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000900" MajorTopicYN="N">Anti-Bacterial Agents</DescriptorName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="Y">drug effects</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005060" MajorTopicYN="N">Europe</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016680" MajorTopicYN="Y">Genome, Bacterial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038622" MajorTopicYN="N">Internationality</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008826" MajorTopicYN="N">Microbial Sensitivity Tests</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Antimicrobial resistance</Keyword><Keyword MajorTopicYN="N">ECOFF</Keyword><Keyword MajorTopicYN="N">Epidemiological cut-off values</Keyword><Keyword MajorTopicYN="N">Next generation sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>11</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>11</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>11</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>2</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>11</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27890457</ArticleId><ArticleId IdType="pii">S1198-743X(16)30568-7</ArticleId><ArticleId IdType="doi">10.1016/j.cmi.2016.11.012</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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