The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.
Identifieur interne : 000174 ( Main/Exploration ); précédent : 000173; suivant : 000175The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.
Auteurs : M J Ellington [Royaume-Uni] ; O. Ekelund [Suède] ; F M Aarestrup [Danemark] ; R. Canton [Espagne] ; M. Doumith [Royaume-Uni] ; C. Giske [Suède] ; H. Grundman [Allemagne] ; H. Hasman [Danemark] ; M T G. Holden [Royaume-Uni] ; K L Hopkins [Royaume-Uni] ; J. Iredell [Australie] ; G. Kahlmeter [Suède] ; C U Köser [Royaume-Uni] ; A. Macgowan [Royaume-Uni] ; D. Mevius [Pays-Bas] ; M. Mulvey [Canada] ; T. Naas [France] ; T. Peto [Royaume-Uni] ; J-M Rolain [France] ; Samuelsen [Norvège] ; N. Woodford [Royaume-Uni]Source :
- Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases [ 1469-0691 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Bactéries.
- pharmacologie : Antibactériens.
- Bactéries, Europe, Génome bactérien, Internationalité, Tests de sensibilité microbienne.
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
Affiliations:
- Allemagne, Australie, Canada, Danemark, Espagne, France, Norvège, Pays-Bas, Royaume-Uni, Suède
- Angleterre, Angleterre de l'Est, Bade-Wurtemberg, Communauté de Madrid, District de Fribourg-en-Brisgau, Grand Londres, Hovedstaden, Oxfordshire, Provence-Alpes-Côte d'Azur, Svealand, Utrecht (province)
- Cambridge, Copenhague, Fribourg-en-Brisgau, Londres, Madrid, Marseille, Oxford, Stockholm, Utrecht
- Université d'Aix-Marseille, Université d'Oxford, Université de Cambridge
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Le document en format XML
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<affiliation wicri:level="1"><nlm:affiliation>School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK.</nlm:affiliation>
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<country xml:lang="fr">Australie</country>
<wicri:regionArea>Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW</wicri:regionArea>
<wicri:noRegion>NSW</wicri:noRegion>
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<author><name sortKey="Kahlmeter, G" sort="Kahlmeter, G" uniqKey="Kahlmeter G" first="G" last="Kahlmeter">G. Kahlmeter</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden.</nlm:affiliation>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö</wicri:regionArea>
<wicri:noRegion>Växjö</wicri:noRegion>
</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 wicri:level="4"><nlm:affiliation>Department of Medicine, University of Cambridge, Cambridge, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Medicine, University of Cambridge, Cambridge</wicri:regionArea>
<orgName type="university">Université de Cambridge</orgName>
<placeName><settlement type="city">Cambridge</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Angleterre de l'Est</region>
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<author><name sortKey="Macgowan, A" sort="Macgowan, A" uniqKey="Macgowan A" first="A" last="Macgowan">A. Macgowan</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol</wicri:regionArea>
<wicri:noRegion>Bristol</wicri:noRegion>
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<author><name sortKey="Mevius, D" sort="Mevius, D" uniqKey="Mevius D" first="D" last="Mevius">D. Mevius</name>
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<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht</wicri:regionArea>
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<country xml:lang="fr">France</country>
<wicri:regionArea>French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre</wicri:regionArea>
<wicri:noRegion>Le Kremlin-Bicêtre</wicri:noRegion>
<wicri:noRegion>Le Kremlin-Bicêtre</wicri:noRegion>
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<author><name sortKey="Peto, T" sort="Peto, T" uniqKey="Peto T" first="T" last="Peto">T. Peto</name>
<affiliation wicri:level="4"><nlm:affiliation>Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford</wicri:regionArea>
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<settlement type="city">Oxford</settlement>
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<orgName type="university">Université d'Oxford</orgName>
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<author><name sortKey="Rolain, J M" sort="Rolain, J M" uniqKey="Rolain J" first="J-M" last="Rolain">J-M Rolain</name>
<affiliation wicri:level="4"><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>
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<wicri:regionArea>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</wicri:regionArea>
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<settlement type="city">Marseille</settlement>
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<orgName type="university">Université d'Aix-Marseille</orgName>
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<author><name sortKey="Samuelsen, " sort="Samuelsen, " uniqKey="Samuelsen " first="" last="Samuelsen"> Samuelsen</name>
<affiliation wicri:level="1"><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>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø</wicri:regionArea>
<wicri:noRegion>Tromsø</wicri:noRegion>
</affiliation>
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<author><name sortKey="Woodford, N" sort="Woodford, N" uniqKey="Woodford N" first="N" last="Woodford">N. Woodford</name>
<affiliation wicri:level="3"><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>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
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<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>
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<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>
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<term>Bactéries ()</term>
<term>Bactéries (génétique)</term>
<term>Europe</term>
<term>Génome bactérien</term>
<term>Internationalité</term>
<term>Tests de sensibilité microbienne ()</term>
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<keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Anti-Bacterial Agents</term>
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<keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Bacteria</term>
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</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Microbial Sensitivity Tests</term>
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<keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antibactériens</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Europe</term>
<term>Genome, Bacterial</term>
<term>Internationality</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Bactéries</term>
<term>Europe</term>
<term>Génome bactérien</term>
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<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>
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<tree><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Ellington, M J" sort="Ellington, M J" uniqKey="Ellington M" first="M J" last="Ellington">M J Ellington</name>
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<country name="Danemark"><noRegion><name sortKey="Aarestrup, F M" sort="Aarestrup, F M" uniqKey="Aarestrup F" first="F M" last="Aarestrup">F M Aarestrup</name>
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<name sortKey="Hasman, H" sort="Hasman, H" uniqKey="Hasman H" first="H" last="Hasman">H. Hasman</name>
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<country name="Allemagne"><region name="Bade-Wurtemberg"><name sortKey="Grundman, H" sort="Grundman, H" uniqKey="Grundman H" first="H" last="Grundman">H. Grundman</name>
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