Whole-genome sequencing for routine pathogen surveillance in public health: A population snapshot of invasive Staphylococcus aureus in Europe

dc.contributorAalto-yliopistofi
dc.contributorAalto Universityen
dc.contributor.authorAanensen, David M.en_US
dc.contributor.authorFeil, Edward J.en_US
dc.contributor.authorHolden, Matthew T Gen_US
dc.contributor.authorDordel, Janinaen_US
dc.contributor.authorYeats, Corin A.en_US
dc.contributor.authorFedosejev, Artemijen_US
dc.contributor.authorGoater, Richarden_US
dc.contributor.authorCastillo-Ramírez, Santiagoen_US
dc.contributor.authorCorander, Jukkaen_US
dc.contributor.authorColijn, Carolineen_US
dc.contributor.authorChlebowicz, Monika A.en_US
dc.contributor.authorSchouls, Leoen_US
dc.contributor.authorHeck, Maxen_US
dc.contributor.authorPluister, Gerlindeen_US
dc.contributor.authorRuimy, Raymonden_US
dc.contributor.authorKahlmeter, Gunnaren_US
dc.contributor.authorÅhman, Jennyen_US
dc.contributor.authorMatuschek, Erikaen_US
dc.contributor.authorFriedrich, Alexander W.en_US
dc.contributor.authorParkhill, Julianen_US
dc.contributor.authorBentley, Stephen D.en_US
dc.contributor.authorSpratt, Brian G.en_US
dc.contributor.authorGrundmann, Hajoen_US
dc.contributor.authorKrziwanek, Karinaen_US
dc.contributor.authorStumvoll, Sabineen_US
dc.contributor.authorKoller, Walteren_US
dc.contributor.authorDenis, Olivieren_US
dc.contributor.authorStruelens, Marcen_US
dc.contributor.authorNashev, Dimitren_US
dc.contributor.authorBudimir, Anaen_US
dc.contributor.authorKalenic, Smiljaen_US
dc.contributor.authorPieridou-Bagatzouni, Despoen_US
dc.contributor.authorJakubu, Vladislaven_US
dc.contributor.authorZemlickova, Helenaen_US
dc.contributor.authorWesth, Henriken_US
dc.contributor.authorLarsen, Anders Rhoden_US
dc.contributor.authorSkov, Roberten_US
dc.contributor.authorLaurent, Fredericen_US
dc.contributor.authorEttienne, Jeromeen_US
dc.contributor.authorStrommenger, Birgiten_US
dc.contributor.authorWitte, Wolfgangen_US
dc.contributor.authorVourli, Sofiaen_US
dc.contributor.authorVatopoulos, Alkisen_US
dc.contributor.authorVainio, Annien_US
dc.contributor.authorVuopio-Varkila, Jaanaen_US
dc.contributor.authorFuzi, Miklosen_US
dc.contributor.authorUngvári, Erikaen_US
dc.contributor.authorMurchan, Stephanen_US
dc.contributor.authorRossney, Angelaen_US
dc.contributor.authorMiklasevics, Edvinsen_US
dc.contributor.authorBalode, Artaen_US
dc.contributor.authorHaraldsson, Gunnsteinnen_US
dc.contributor.authorKristinsson, Karl G.en_US
dc.contributor.authorMonaco, Monicaen_US
dc.contributor.authorPantosti, Annalisaen_US
dc.contributor.authorBorg, Michaelen_US
dc.contributor.authorVan Santen-Verheuvel, Margaen_US
dc.contributor.authorHuijsdens, Xanderen_US
dc.contributor.authorMarstein, Lillianen_US
dc.contributor.authorJacobsen, Tronden_US
dc.contributor.authorSimonsen, Gunnar Skoven_US
dc.contributor.authorAiresde-Sousa, Martaen_US
dc.contributor.authorDe Lencastre, Herminiaen_US
dc.contributor.authorLuczak-Kadlubowska, Agnieszkaen_US
dc.contributor.authorHryniewicz, Waleriaen_US
dc.contributor.authorStraut, Monicaen_US
dc.contributor.authorCodita, Irinaen_US
dc.contributor.authorPerez-Vazquez, Mariaen_US
dc.contributor.authorIglesias, Jesus Oteoen_US
dc.contributor.authorSpik, Vesna Cvitkovicen_US
dc.contributor.authorMueller-Premru, Manicaen_US
dc.contributor.authorHaeggman, Saraen_US
dc.contributor.authorOlsson-Liljequist, Barbroen_US
dc.contributor.authorEllington, Matthewen_US
dc.contributor.authorKearns, Angelaen_US
dc.contributor.departmentDepartment of Computer Scienceen
dc.contributor.groupauthorMyllymäki Petri group (HIIT)en
dc.contributor.groupauthorHelsinki Institute for Information Technology (HIIT)en
dc.contributor.organizationCentre for Genomic Pathogen Surveillanceen_US
dc.contributor.organizationUniversity of Bathen_US
dc.contributor.organizationUniversity of St Andrewsen_US
dc.contributor.organizationDrexel Universityen_US
dc.contributor.organizationUniversidad Nacional Autónoma de Méxicoen_US
dc.contributor.organizationImperial College Londonen_US
dc.contributor.organizationUniversity of Groningenen_US
dc.contributor.organizationNational Institute of Public Health and the Environmenten_US
dc.contributor.organizationCHU de Niceen_US
dc.contributor.organizationEUCAST Development Laboratoryen_US
dc.contributor.organizationWellcome Trusten_US
dc.contributor.organizationAlbert-Ludwigs-Universität Freiburgen_US
dc.contributor.organizationNational Reference Centre for Nosocomial Infections and Antimicrobial Resistanceen_US
dc.contributor.organizationKlinisches Institut für Hygiene und Medizinische Mikrobiologieen_US
dc.contributor.organizationUniversité libre de Bruxellesen_US
dc.contributor.organizationNational Center of Infectious and Parasitic Diseases Bulgariaen_US
dc.contributor.organizationUniversity of Zagreben_US
dc.contributor.organizationNicosia General Hospitalen_US
dc.contributor.organizationCzech National Institute of Public Healthen_US
dc.contributor.organizationUniversity of Copenhagenen_US
dc.contributor.organizationStatens Serum Instituten_US
dc.contributor.organizationInstitut national de la santé et de la recherche médicaleen_US
dc.contributor.organizationRobert Koch-Instituten_US
dc.contributor.organizationNational School of Public Healthen_US
dc.contributor.organizationFinnish Institute for Health and Welfare (THL)en_US
dc.contributor.organizationSemmelweis Universityen_US
dc.contributor.organizationAgricultural Biotechnology Center Godolloen_US
dc.contributor.organizationHealth Protection Surveillance Centreen_US
dc.contributor.organizationTrinity College Dublinen_US
dc.contributor.organizationPauls Stradins Clinical University Hospitalen_US
dc.contributor.organizationUniversity of Icelanden_US
dc.contributor.organizationIstituto Superiore di Sanitàen_US
dc.contributor.organizationMater Dei Hospitalen_US
dc.contributor.organizationNorwegian University of Science and Technologyen_US
dc.contributor.organizationUniversity Hospital of North Norwayen_US
dc.contributor.organizationEscola Superior de Saude da Cruz Vermelha Portuguesaen_US
dc.contributor.organizationRockefeller Universityen_US
dc.contributor.organizationCentre of Quality Control in Microbiologyen_US
dc.contributor.organizationNational Medicines Institute, Warsawen_US
dc.contributor.organizationDr. I. Cantacuzino Instituteen_US
dc.contributor.organizationInstituto de Salud Carlos IIIen_US
dc.contributor.organizationSwedish Institute for Infectious Disease Controlen_US
dc.contributor.organizationAntimicrobial Resistance and Healthcare Associated Infections Reference Uniten_US
dc.date.accessioned2017-05-11T08:21:48Z
dc.date.available2017-05-11T08:21:48Z
dc.date.issued2016-05-01en_US
dc.description.abstractThe 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) communityoriented 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 wholegenome 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.en
dc.description.versionPeer revieweden
dc.format.extent15
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationAanensen, D M, Feil, E J, Holden, M T G, Dordel, J, Yeats, C A, Fedosejev, A, Goater, R, Castillo-Ramírez, S, Corander, J, Colijn, C, Chlebowicz, M A, Schouls, L, Heck, M, Pluister, G, Ruimy, R, Kahlmeter, G, Åhman, J, Matuschek, E, Friedrich, A W, Parkhill, J, Bentley, S D, Spratt, B G, Grundmann, H, Krziwanek, K, Stumvoll, S, Koller, W, Denis, O, Struelens, M, Nashev, D, Budimir, A, Kalenic, S, Pieridou-Bagatzouni, D, Jakubu, V, Zemlickova, H, Westh, H, Larsen, A R, Skov, R, Laurent, F, Ettienne, J, Strommenger, B, Witte, W, Vourli, S, Vatopoulos, A, Vainio, A, Vuopio-Varkila, J, Fuzi, M, Ungvári, E, Murchan, S, Rossney, A, Miklasevics, E, Balode, A, Haraldsson, G, Kristinsson, K G, Monaco, M, Pantosti, A, Borg, M, Van Santen-Verheuvel, M, Huijsdens, X, Marstein, L, Jacobsen, T, Simonsen, G S, Airesde-Sousa, M, De Lencastre, H, Luczak-Kadlubowska, A, Hryniewicz, W, Straut, M, Codita, I, Perez-Vazquez, M, Iglesias, J O, Spik, V C, Mueller-Premru, M, Haeggman, S, Olsson-Liljequist, B, Ellington, M & Kearns, A 2016, ' Whole-genome sequencing for routine pathogen surveillance in public health : A population snapshot of invasive Staphylococcus aureus in Europe ', MBIO, vol. 7, no. 3, e00444-16 . https://doi.org/10.1128/mBio.00444-16en
dc.identifier.doi10.1128/mBio.00444-16en_US
dc.identifier.issn2161-2129
dc.identifier.otherPURE UUID: 6c5b4758-9bec-4c0b-ae2c-343b48b9c48den_US
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dc.identifier.urihttps://aaltodoc.aalto.fi/handle/123456789/25589
dc.identifier.urnURN:NBN:fi:aalto-201705113973
dc.language.isoenen
dc.relation.ispartofseriesMBIOen
dc.relation.ispartofseriesVolume 7, issue 3en
dc.rightsopenAccessen
dc.titleWhole-genome sequencing for routine pathogen surveillance in public health: A population snapshot of invasive Staphylococcus aureus in Europeen
dc.typeA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessäfi
dc.type.versionpublishedVersion
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