de Knegt, Leonardo Victor

Kudirkiene, Egle

Nielsen, Liza R.

Olsen, John E.

Sørensen, Gitte

Online Research Database In Technology

                       General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.  • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal   If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.     Downloaded from orbit.dtu.dk on: Dec 18, 2017Genetic clusters and circulation of Salmonella Dublin in Jutlandde Knegt, Leonardo Victor; Kudirkiene, Egle; Sørensen, Gitte; Nielsen, Liza R.; Olsen, John E.Publication date:2017Document VersionPublisher's PDF, also known as Version of recordLink back to DTU OrbitCitation (APA):de Knegt, L. V., Kudirkiene, E., Sørensen, G., Nielsen, L. R., & Olsen, J. E. (2017). Genetic clusters andcirculation of Salmonella Dublin in Jutland. Poster session presented at 2017 Annual Meeting of SVEPM 2017,29-31 March, Inverness, Scotland, Scotland, United Kingdom.F A C U L T Y   O F   H E A L T H   A N D   M E D I C A L   S C I E N C E SU N I V E R S I T Y   O F  C O P E N H A G E NRESULTSGenetic clusters and circulation    of Salmonella Dublin in JutlandLeonardo V. de Knegt1, Egle Kudirkiene1, Gitte Sørensen2, Liza R. Nielsen1, John E. Olsen11 Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark, leonardo@sund.ku.dk2 National Food Institute, Technical University of Denmark / Statens Serum Institut, DenmarkThe study was funded by The Danish Agriculture Levy Fund SVEPM 2017, InvernessExample of movement networkCore genome differences discard false circulation nodesSerology helps discard negative intermediariesKey herds indicate possible contact points between Clusters II and IIIPlasmid sharing highlights non-visible contacts between genomically different or trade-isolated herdsLocation of herds by cluster and plasmid profile (colours)Trade network centeredaround marketsPlasmid profilingIIIIIICore genome clustersLettersA to ZWindicatesampledherdsCluster ICluster IICluster IIIMarketsFADCSPAARRCluster III Mid- and South JutlandCluster IImostly North, heavily enriched by plasmidsCluster I highly distant, may be ancestral Danish strainsBACKGROUND2002: Danish S. Dublin surveillance program2007: National eradication programme initiated2010: Enforced trade restrictions in legislation2013: Mandatory control and strict trade restrictions METHODS• S. Dublin: 197 isolates from 58 herds 1996 to 2016• Sequencing: MiSeq 250 bp pair-end • Assembly/Annotation: SPADEs 3.9.1./Prokka 1.0• Population structure analysis: CSI Phylogeny• Genome content analysis: Roary/Scoary• Movement of cattle between herds since 1994: from Danish Cattle DatabaseCHALLENGEContinued circulation of S. Dublin, but cattle movements too intricate to detect clear circulation patterns based on existing data. Many herds interconnected by 1st or 2nd or higher degree contactsOBJECTIVE To use whole genome sequencing (WGS) to improve the understanding of strain circulation between herds

Genetic clusters and circulation of <em>Salmonella</em> Dublin in Jutland

Sorensen, Gitte

Nielsen, Liza Rosenbaum

Olsen, John Elmerdahl

Copenhagen University Research Information System

u n i ve r s i t y  o f  co pe n h ag e n  Københavns UniversitetGenetic clusters and circulation of Salmonella Dublin in Jutlandde Knegt, Leonardo Victor; Kudirkiene, Egle; Sorensen, Gitte; Nielsen, Liza Rosenbaum;Olsen, John ElmerdahlPublication date:2017Document versionPeer reviewed versionCitation for published version (APA):de Knegt, L. V., Kudirkiene, E., Sorensen, G., Nielsen, L. R., & Olsen, J. E. (2017). Genetic clusters andcirculation of Salmonella Dublin in Jutland. Poster session presented at SVEPM2017: The Annual Meeting of theSociety for Veterinary Epidemiology and Preventive Medicine , Inverness, United Kingdom.Download date: 03. Feb. 2020F A C U L T Y   O F   H E A L T H   A N D   M E D I C A L   S C I E N C E SU N I V E R S I T Y   O F  C O P E N H A G E NRESULTSGenetic clusters and circulation    of Salmonella Dublin in JutlandLeonardo V. de Knegt1, Egle Kudirkiene1, Gitte Sørensen2, Liza R. Nielsen1, John E. Olsen11 Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark, leonardo@sund.ku.dk2 National Food Institute, Technical University of Denmark / Statens Serum Institut, DenmarkThe study was funded by The Danish Agriculture Levy Fund SVEPM 2017, InvernessExample of movement networkCore genome differences discard false circulation nodesSerology helps discard negative intermediariesKey herds indicate possible contact points between Clusters II and IIIPlasmid sharing highlights non-visible contacts between genomically different or trade-isolated herdsLocation of herds by cluster and plasmid profile (colours)Trade network centeredaround marketsPlasmid profilingIIIIIICore genome clustersLettersA to ZWindicatesampledherdsCluster ICluster IICluster IIIMarketsFADCSPAARRCluster III Mid- and South JutlandCluster IImostly North, heavily enriched by plasmidsCluster I highly distant, may be ancestral Danish strainsBACKGROUND2002: Danish S. Dublin surveillance program2007: National eradication programme initiated2010: Enforced trade restrictions in legislation2013: Mandatory control and strict trade restrictions METHODS• S. Dublin: 197 isolates from 58 herds 1996 to 2016• Sequencing: MiSeq 250 bp pair-end • Assembly/Annotation: SPADEs 3.9.1./Prokka 1.0• Population structure analysis: CSI Phylogeny• Genome content analysis: Roary/Scoary• Movement of cattle between herds since 1994: from Danish Cattle DatabaseCHALLENGEContinued circulation of S. Dublin, but cattle movements too intricate to detect clear circulation patterns based on existing data. Many herds interconnected by 1st or 2nd or higher degree contactsOBJECTIVE To use whole genome sequencing (WGS) to improve the understanding of strain circulation between herds

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http://orbit.dtu.dk/ws/files/132995696/deKnegt_Genetic_clusters_and_circulation_of_Salmonella_Dublin_in_Jutland_1_.pdf

Genetic clusters and circulation of <em>Salmonella</em> Dublin in Jutland

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