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Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe
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 Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epidemiologic...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959656/ https://www.ncbi.nlm.nih.gov/pubmed/27150362 http://dx.doi.org/10.1128/mBio.00444-16 |
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author | Aanensen, David M. Feil, Edward J. Holden, Matthew T. G. Dordel, Janina Yeats, Corin A. Fedosejev, Artemij Goater, Richard Castillo-Ramírez, Santiago Corander, Jukka Colijn, Caroline Chlebowicz, Monika A. Schouls, Leo Heck, Max Pluister, Gerlinde Ruimy, Raymond Kahlmeter, Gunnar Åhman, Jenny Matuschek, Erika Friedrich, Alexander W. Parkhill, Julian Bentley, Stephen D. Spratt, Brian G. Grundmann, Hajo |
author_facet | Aanensen, David M. Feil, Edward J. Holden, Matthew T. G. Dordel, Janina Yeats, Corin A. Fedosejev, Artemij Goater, Richard Castillo-Ramírez, Santiago Corander, Jukka Colijn, Caroline Chlebowicz, Monika A. Schouls, Leo Heck, Max Pluister, Gerlinde Ruimy, Raymond Kahlmeter, Gunnar Åhman, Jenny Matuschek, Erika Friedrich, Alexander W. Parkhill, Julian Bentley, Stephen D. Spratt, Brian G. Grundmann, Hajo |
author_sort | Aanensen, David M. |
collection | PubMed |
description | 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 Staphylococcus aureus 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 (http://www.microreact.org/project/EkUvg9uY?tt=rc). 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 in silico 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. |
format | Online Article Text |
id | pubmed-4959656 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-49596562016-07-25 Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe Aanensen, David M. Feil, Edward J. Holden, Matthew T. G. Dordel, Janina Yeats, Corin A. Fedosejev, Artemij Goater, Richard Castillo-Ramírez, Santiago Corander, Jukka Colijn, Caroline Chlebowicz, Monika A. Schouls, Leo Heck, Max Pluister, Gerlinde Ruimy, Raymond Kahlmeter, Gunnar Åhman, Jenny Matuschek, Erika Friedrich, Alexander W. Parkhill, Julian Bentley, Stephen D. Spratt, Brian G. Grundmann, Hajo mBio Research Article 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 Staphylococcus aureus 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 (http://www.microreact.org/project/EkUvg9uY?tt=rc). 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 in silico 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. American Society for Microbiology 2016-05-05 /pmc/articles/PMC4959656/ /pubmed/27150362 http://dx.doi.org/10.1128/mBio.00444-16 Text en Copyright © 2016 Aanensen et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Research Article Aanensen, David M. Feil, Edward J. Holden, Matthew T. G. Dordel, Janina Yeats, Corin A. Fedosejev, Artemij Goater, Richard Castillo-Ramírez, Santiago Corander, Jukka Colijn, Caroline Chlebowicz, Monika A. Schouls, Leo Heck, Max Pluister, Gerlinde Ruimy, Raymond Kahlmeter, Gunnar Åhman, Jenny Matuschek, Erika Friedrich, Alexander W. Parkhill, Julian Bentley, Stephen D. Spratt, Brian G. Grundmann, Hajo Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe |
title | Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe |
title_full | Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe |
title_fullStr | Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe |
title_full_unstemmed | Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe |
title_short | Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe |
title_sort | whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive staphylococcus aureus in europe |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959656/ https://www.ncbi.nlm.nih.gov/pubmed/27150362 http://dx.doi.org/10.1128/mBio.00444-16 |
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