Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe
Identifieur interne : 000000 ( Main/Merge ); suivant : 000001Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe
Auteurs : David M. Aanensen [Royaume-Uni] ; Edward J. Feil [Royaume-Uni] ; Matthew T. G. Holden [Royaume-Uni] ; Janina Dordel [Royaume-Uni, États-Unis] ; Corin A. Yeats [Royaume-Uni] ; Artemij Fedosejev [Royaume-Uni] ; Richard Goater [Royaume-Uni] ; Santiago Castillo-Ramírez [Mexique] ; Jukka Corander [Finlande] ; Caroline Colijn [Royaume-Uni] ; Monika A. Chlebowicz [Pays-Bas] ; Leo Schouls [Pays-Bas] ; Max Heck [Pays-Bas] ; Gerlinde Pluister [Pays-Bas] ; Raymond Ruimy [France] ; Gunnar Kahlmeter [Suède] ; Jenny Hman [Suède] ; Erika Matuschek [Suède] ; Alexander W. Friedrich [Pays-Bas] ; Julian Parkhill [Royaume-Uni] ; Stephen D. Bentley [Royaume-Uni] ; Brian G. Spratt [Royaume-Uni] ; Hajo Grundmann [Pays-Bas, Allemagne]Source :
- mBio [ 2150-7511 ] ; 2016.
Abstract
The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive
Url:
DOI: 10.1128/mBio.00444-16
PubMed: 27150362
PubMed Central: 4959656
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PMC:4959656Le document en format XML
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<author><name sortKey="Fedosejev, Artemij" sort="Fedosejev, Artemij" uniqKey="Fedosejev A" first="Artemij" last="Fedosejev">Artemij Fedosejev</name>
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<author><name sortKey="Colijn, Caroline" sort="Colijn, Caroline" uniqKey="Colijn C" first="Caroline" last="Colijn">Caroline Colijn</name>
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<author><name sortKey="Chlebowicz, Monika A" sort="Chlebowicz, Monika A" uniqKey="Chlebowicz M" first="Monika A." last="Chlebowicz">Monika A. Chlebowicz</name>
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</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
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<author><name sortKey="Schouls, Leo" sort="Schouls, Leo" uniqKey="Schouls L" first="Leo" last="Schouls">Leo Schouls</name>
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<author><name sortKey="Heck, Max" sort="Heck, Max" uniqKey="Heck M" first="Max" last="Heck">Max Heck</name>
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<author><name sortKey="Ruimy, Raymond" sort="Ruimy, Raymond" uniqKey="Ruimy R" first="Raymond" last="Ruimy">Raymond Ruimy</name>
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<author><name sortKey="Kahlmeter, Gunnar" sort="Kahlmeter, Gunnar" uniqKey="Kahlmeter G" first="Gunnar" last="Kahlmeter">Gunnar Kahlmeter</name>
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<author><name sortKey=" Hman, Jenny" sort=" Hman, Jenny" uniqKey=" Hman J" first="Jenny" last=" Hman">Jenny Hman</name>
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<country xml:lang="fr">Suède</country>
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<author><name sortKey="Matuschek, Erika" sort="Matuschek, Erika" uniqKey="Matuschek E" first="Erika" last="Matuschek">Erika Matuschek</name>
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<country xml:lang="fr">Suède</country>
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<author><name sortKey="Friedrich, Alexander W" sort="Friedrich, Alexander W" uniqKey="Friedrich A" first="Alexander W." last="Friedrich">Alexander W. Friedrich</name>
<affiliation wicri:level="3"><nlm:aff id="aff10"><addr-line>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen, The Netherlands</addr-line>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen</wicri:regionArea>
<placeName><settlement type="city">Groningue</settlement>
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<author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
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<author><name sortKey="Bentley, Stephen D" sort="Bentley, Stephen D" uniqKey="Bentley S" first="Stephen D." last="Bentley">Stephen D. Bentley</name>
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</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
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<author><name sortKey="Spratt, Brian G" sort="Spratt, Brian G" uniqKey="Spratt B" first="Brian G." last="Spratt">Brian G. Spratt</name>
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</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
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<author><name sortKey="Grundmann, Hajo" sort="Grundmann, Hajo" uniqKey="Grundmann H" first="Hajo" last="Grundmann">Hajo Grundmann</name>
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</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen</wicri:regionArea>
<placeName><settlement type="city">Groningue</settlement>
<region nuts="2" type="province">Groningue (province)</region>
</placeName>
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<affiliation wicri:level="3"><nlm:aff id="aff14"><addr-line>Department of Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany</addr-line>
</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Department of Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <italic>Staphylococcus aureus</italic>
in Europe</title>
<author><name sortKey="Aanensen, David M" sort="Aanensen, David M" uniqKey="Aanensen D" first="David M." last="Aanensen">David M. Aanensen</name>
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</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, 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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<affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge</wicri:regionArea>
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<author><name sortKey="Feil, Edward J" sort="Feil, Edward J" uniqKey="Feil E" first="Edward J." last="Feil">Edward J. Feil</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
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<wicri:noRegion>Bath</wicri:noRegion>
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<author><name sortKey="Holden, Matthew T G" sort="Holden, Matthew T G" uniqKey="Holden M" first="Matthew T. G." last="Holden">Matthew T. G. Holden</name>
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</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>School of Medicine, University of St. Andrews, St. Andrews</wicri:regionArea>
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<affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea>
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<author><name sortKey="Dordel, Janina" sort="Dordel, Janina" uniqKey="Dordel J" first="Janina" last="Dordel">Janina Dordel</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
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<wicri:noRegion>Cambridge</wicri:noRegion>
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<affiliation wicri:level="2"><nlm:aff id="aff6"><addr-line>Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biology, Drexel University, Philadelphia, Pennsylvania</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yeats, Corin A" sort="Yeats, Corin A" uniqKey="Yeats C" first="Corin A." last="Yeats">Corin A. Yeats</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London</wicri:regionArea>
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</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Fedosejev, Artemij" sort="Fedosejev, Artemij" uniqKey="Fedosejev A" first="Artemij" last="Fedosejev">Artemij Fedosejev</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Goater, Richard" sort="Goater, Richard" uniqKey="Goater R" first="Richard" last="Goater">Richard Goater</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Castillo Ramirez, Santiago" sort="Castillo Ramirez, Santiago" uniqKey="Castillo Ramirez S" first="Santiago" last="Castillo-Ramírez">Santiago Castillo-Ramírez</name>
<affiliation wicri:level="1"><nlm:aff id="aff7"><addr-line>Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico</addr-line>
</nlm:aff>
<country xml:lang="fr">Mexique</country>
<wicri:regionArea>Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos</wicri:regionArea>
<wicri:noRegion>Morelos</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Corander, Jukka" sort="Corander, Jukka" uniqKey="Corander J" first="Jukka" last="Corander">Jukka Corander</name>
<affiliation wicri:level="1"><nlm:aff id="aff8"><addr-line>Helsinki Institute for Information Technology HIIT, Aalto, Finland</addr-line>
</nlm:aff>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Helsinki Institute for Information Technology HIIT, Aalto</wicri:regionArea>
<wicri:noRegion>Aalto</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Colijn, Caroline" sort="Colijn, Caroline" uniqKey="Colijn C" first="Caroline" last="Colijn">Caroline Colijn</name>
<affiliation wicri:level="3"><nlm:aff id="aff9"><addr-line>Department of Mathematics, Imperial College London, London, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Mathematics, Imperial College London, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Chlebowicz, Monika A" sort="Chlebowicz, Monika A" uniqKey="Chlebowicz M" first="Monika A." last="Chlebowicz">Monika A. Chlebowicz</name>
<affiliation wicri:level="3"><nlm:aff id="aff10"><addr-line>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen, The Netherlands</addr-line>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen</wicri:regionArea>
<placeName><settlement type="city">Groningue</settlement>
<region nuts="2" type="province">Groningue (province)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Schouls, Leo" sort="Schouls, Leo" uniqKey="Schouls L" first="Leo" last="Schouls">Leo Schouls</name>
<affiliation wicri:level="1"><nlm:aff id="aff11"><addr-line>National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</addr-line>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea>
<wicri:noRegion>Bilthoven</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Heck, Max" sort="Heck, Max" uniqKey="Heck M" first="Max" last="Heck">Max Heck</name>
<affiliation wicri:level="1"><nlm:aff id="aff11"><addr-line>National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</addr-line>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea>
<wicri:noRegion>Bilthoven</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pluister, Gerlinde" sort="Pluister, Gerlinde" uniqKey="Pluister G" first="Gerlinde" last="Pluister">Gerlinde Pluister</name>
<affiliation wicri:level="1"><nlm:aff id="aff11"><addr-line>National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</addr-line>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea>
<wicri:noRegion>Bilthoven</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ruimy, Raymond" sort="Ruimy, Raymond" uniqKey="Ruimy R" first="Raymond" last="Ruimy">Raymond Ruimy</name>
<affiliation wicri:level="1"><nlm:aff id="aff12"><addr-line>Centre Hospitalier Universitaire de Nice, Nice, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Centre Hospitalier Universitaire de Nice, Nice</wicri:regionArea>
<placeName><settlement type="city">Nice</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Kahlmeter, Gunnar" sort="Kahlmeter, Gunnar" uniqKey="Kahlmeter G" first="Gunnar" last="Kahlmeter">Gunnar Kahlmeter</name>
<affiliation wicri:level="1"><nlm:aff id="aff13"><addr-line>EUCAST Development Laboratory, Växjö, Sweden</addr-line>
</nlm:aff>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>EUCAST Development Laboratory, Växjö</wicri:regionArea>
<wicri:noRegion>Växjö</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey=" Hman, Jenny" sort=" Hman, Jenny" uniqKey=" Hman J" first="Jenny" last=" Hman">Jenny Hman</name>
<affiliation wicri:level="1"><nlm:aff id="aff13"><addr-line>EUCAST Development Laboratory, Växjö, Sweden</addr-line>
</nlm:aff>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>EUCAST Development Laboratory, Växjö</wicri:regionArea>
<wicri:noRegion>Växjö</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Matuschek, Erika" sort="Matuschek, Erika" uniqKey="Matuschek E" first="Erika" last="Matuschek">Erika Matuschek</name>
<affiliation wicri:level="1"><nlm:aff id="aff13"><addr-line>EUCAST Development Laboratory, Växjö, Sweden</addr-line>
</nlm:aff>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>EUCAST Development Laboratory, Växjö</wicri:regionArea>
<wicri:noRegion>Växjö</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Friedrich, Alexander W" sort="Friedrich, Alexander W" uniqKey="Friedrich A" first="Alexander W." last="Friedrich">Alexander W. Friedrich</name>
<affiliation wicri:level="3"><nlm:aff id="aff10"><addr-line>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen, The Netherlands</addr-line>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen</wicri:regionArea>
<placeName><settlement type="city">Groningue</settlement>
<region nuts="2" type="province">Groningue (province)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Bentley, Stephen D" sort="Bentley, Stephen D" uniqKey="Bentley S" first="Stephen D." last="Bentley">Stephen D. Bentley</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Spratt, Brian G" sort="Spratt, Brian G" uniqKey="Spratt B" first="Brian G." last="Spratt">Brian G. Spratt</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Grundmann, Hajo" sort="Grundmann, Hajo" uniqKey="Grundmann H" first="Hajo" last="Grundmann">Hajo Grundmann</name>
<affiliation wicri:level="3"><nlm:aff id="aff10"><addr-line>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen, The Netherlands</addr-line>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen</wicri:regionArea>
<placeName><settlement type="city">Groningue</settlement>
<region nuts="2" type="province">Groningue (province)</region>
</placeName>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="aff14"><addr-line>Department of Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany</addr-line>
</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Department of Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
<settlement type="city">Fribourg-en-Brisgau</settlement>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">mBio</title>
<idno type="eISSN">2150-7511</idno>
<imprint><date when="2016">2016</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><title>ABSTRACT</title>
<p>The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive <italic>Staphylococcus aureus</italic>
isolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (<ext-link ext-link-type="uri" xlink:href="http://www.microreact.org/project/EkUvg9uY?tt=rc">http://www.microreact.org/project/EkUvg9uY?tt=rc</ext-link>
). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show that <italic>in silico</italic>
predictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools.</p>
</div>
</front>
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</author>
<author><name sortKey="Smith, Nh" uniqKey="Smith N">NH Smith</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cant N, R" uniqKey="Cant N R">R Cantón</name>
</author>
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</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grundmann, H" uniqKey="Grundmann H">H Grundmann</name>
</author>
<author><name sortKey="Aanensen, Dm" uniqKey="Aanensen D">DM Aanensen</name>
</author>
<author><name sortKey="Van Den Wijngaard, Cc" uniqKey="Van Den Wijngaard C">CC van den Wijngaard</name>
</author>
<author><name sortKey="Spratt, Bg" uniqKey="Spratt B">BG Spratt</name>
</author>
<author><name sortKey="Harmsen, D" uniqKey="Harmsen D">D Harmsen</name>
</author>
<author><name sortKey="Friedrich, Aw" uniqKey="Friedrich A">AW Friedrich</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Feil, Ej" uniqKey="Feil E">EJ Feil</name>
</author>
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</biblStruct>
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