Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe

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 Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epid...

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Autores principales:	David M. Aanensen, Edward J. Feil, Matthew T. G. Holden, Janina Dordel, Corin A. Yeats, Artemij Fedosejev, Richard Goater, Santiago Castillo-Ramírez, Jukka Corander, Caroline Colijn, Monika A. Chlebowicz, Leo Schouls, Max Heck, Gerlinde Pluister, Raymond Ruimy, Gunnar Kahlmeter, Jenny Åhman, Erika Matuschek, Alexander W. Friedrich, Julian Parkhill, Stephen D. Bentley, Brian G. Spratt, Hajo Grundmann
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/d98f89057f1f4090810ca2b442afb18c
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spelling	oai:doaj.org-article:d98f89057f1f4090810ca2b442afb18c2021-11-15T15:50:16ZWhole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe10.1128/mBio.00444-162150-7511https://doaj.org/article/d98f89057f1f4090810ca2b442afb18c2016-07-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00444-16https://doaj.org/toc/2150-7511ABSTRACT 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. IMPORTANCE The spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.David M. AanensenEdward J. FeilMatthew T. G. HoldenJanina DordelCorin A. YeatsArtemij FedosejevRichard GoaterSantiago Castillo-RamírezJukka CoranderCaroline ColijnMonika A. ChlebowiczLeo SchoulsMax HeckGerlinde PluisterRaymond RuimyGunnar KahlmeterJenny ÅhmanErika MatuschekAlexander W. FriedrichJulian ParkhillStephen D. BentleyBrian G. SprattHajo GrundmannAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 7, Iss 3 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 David M. Aanensen Edward J. Feil Matthew T. G. Holden Janina Dordel Corin A. Yeats Artemij Fedosejev Richard Goater Santiago Castillo-Ramírez Jukka Corander Caroline Colijn Monika A. Chlebowicz Leo Schouls Max Heck Gerlinde Pluister Raymond Ruimy Gunnar Kahlmeter Jenny Åhman Erika Matuschek Alexander W. Friedrich Julian Parkhill Stephen D. Bentley Brian G. Spratt Hajo Grundmann Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe
description	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 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. IMPORTANCE The spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.
format	article
author	David M. Aanensen Edward J. Feil Matthew T. G. Holden Janina Dordel Corin A. Yeats Artemij Fedosejev Richard Goater Santiago Castillo-Ramírez Jukka Corander Caroline Colijn Monika A. Chlebowicz Leo Schouls Max Heck Gerlinde Pluister Raymond Ruimy Gunnar Kahlmeter Jenny Åhman Erika Matuschek Alexander W. Friedrich Julian Parkhill Stephen D. Bentley Brian G. Spratt Hajo Grundmann
author_facet	David M. Aanensen Edward J. Feil Matthew T. G. Holden Janina Dordel Corin A. Yeats Artemij Fedosejev Richard Goater Santiago Castillo-Ramírez Jukka Corander Caroline Colijn Monika A. Chlebowicz Leo Schouls Max Heck Gerlinde Pluister Raymond Ruimy Gunnar Kahlmeter Jenny Åhman Erika Matuschek Alexander W. Friedrich Julian Parkhill Stephen D. Bentley Brian G. Spratt Hajo Grundmann
author_sort	David M. Aanensen
title	Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe
title_short	Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe
title_full	Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe
title_fullStr	Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe
title_full_unstemmed	Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe
title_sort	whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive <named-content content-type="genus-species">staphylococcus aureus</named-content> in europe
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/d98f89057f1f4090810ca2b442afb18c
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Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</named-content> in Europe

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