The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis
Haemophilus parasuis is the etiologic agent of Glässer's disease in pigs and causes devastating losses to the farming industry. Whilst some hyper-virulent isolates have been described, the relationship between genetics and disease outcome has been only partially established. In particular, ther...
| Autores: | , , , , , , , , , , , , , , , , , |
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| Tipo de recurso: | artículo |
| Fecha de publicación: | 2014 |
| País: | España |
| Institución: | Universitat Autònoma de Barcelona |
| Repositorio: | Dipòsit Digital de Documents de la UAB |
| Idioma: | inglés |
| OAI Identifier: | oai:ddd.uab.cat:254630 |
| Acceso en línea: | https://ddd.uab.cat/record/254630 https://dx.doi.org/urn:doi:10.1186/1471-2164-15-1179 |
| Access Level: | acceso abierto |
| Palabra clave: | Genome wide association study Pan-genome Recombination DAPC Virulence factors Population structure Haemophilus parasuis |
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The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuisHowell, Kate J.Weinert, Lucy A.Chaudhuri, Roy R.Luan, Shi-LuPeters, Sarah E.Corander, JukkaHarris, DavidAngen, ØysteinAragón, Virginia|||0000-0002-3470-6015Bensaid, Albert|||0000-0001-6493-3756Williamson, Susanna M.Parkhill, JulianLangford, Paul R.Rycroft, Andrew N.Wren, Brendan W.Holden, Matthew T. G.Tucker, Alexander W.Maskell, Duncan J..Genome wide association studyPan-genomeRecombinationDAPCVirulence factorsPopulation structureHaemophilus parasuisHaemophilus parasuis is the etiologic agent of Glässer's disease in pigs and causes devastating losses to the farming industry. Whilst some hyper-virulent isolates have been described, the relationship between genetics and disease outcome has been only partially established. In particular, there is weak correlation between serovar and disease phenotype. We sequenced the genomes of 212 isolates of H. parasuis and have used this to describe the pan-genome and to correlate this with clinical and carrier status, as well as with serotype. Recombination and population structure analyses identified five groups with very high rates of recombination, separated into two clades of H. parasuis with no signs of recombination between them. We used genome-wide association methods including discriminant analysis of principal components (DAPC) and generalised linear modelling (glm) to look for genetic determinants of this population partition, serovar and pathogenicity. We were able to identify genes from the accessory genome that were significantly associated with phenotypes such as potential serovar specific genes including capsule genes, and 48 putative virulence factors that were significantly different between the clinical and non-clinical isolates. We also show that the presence of many previously suggested virulence factors is not an appropriate marker of virulence. These genes will inform the generation of new molecular diagnostics and vaccines, and refinement of existing typing schemes and show the importance of the accessory genome of a diverse species when investigating the relationship between genotypes and phenotypes. The online version of this article (doi:10.1186/1471-2164-15-1179) contains supplementary material, which is available to authorized users. 22014-01-0120142014-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/254630https://dx.doi.org/urn:doi:10.1186/1471-2164-15-1179reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2546302026-06-06T12:50:31Z |
| dc.title.none.fl_str_mv |
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis |
| title |
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis |
| spellingShingle |
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis Howell, Kate J. Genome wide association study Pan-genome Recombination DAPC Virulence factors Population structure Haemophilus parasuis |
| title_short |
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis |
| title_full |
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis |
| title_fullStr |
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis |
| title_full_unstemmed |
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis |
| title_sort |
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis |
| dc.creator.none.fl_str_mv |
Howell, Kate J. Weinert, Lucy A. Chaudhuri, Roy R. Luan, Shi-Lu Peters, Sarah E. Corander, Jukka Harris, David Angen, Øystein Aragón, Virginia|||0000-0002-3470-6015 Bensaid, Albert|||0000-0001-6493-3756 Williamson, Susanna M. Parkhill, Julian Langford, Paul R. Rycroft, Andrew N. Wren, Brendan W. Holden, Matthew T. G. Tucker, Alexander W. Maskell, Duncan J.. |
| author |
Howell, Kate J. |
| author_facet |
Howell, Kate J. Weinert, Lucy A. Chaudhuri, Roy R. Luan, Shi-Lu Peters, Sarah E. Corander, Jukka Harris, David Angen, Øystein Aragón, Virginia|||0000-0002-3470-6015 Bensaid, Albert|||0000-0001-6493-3756 Williamson, Susanna M. Parkhill, Julian Langford, Paul R. Rycroft, Andrew N. Wren, Brendan W. Holden, Matthew T. G. Tucker, Alexander W. Maskell, Duncan J.. |
| author_role |
author |
| author2 |
Weinert, Lucy A. Chaudhuri, Roy R. Luan, Shi-Lu Peters, Sarah E. Corander, Jukka Harris, David Angen, Øystein Aragón, Virginia|||0000-0002-3470-6015 Bensaid, Albert|||0000-0001-6493-3756 Williamson, Susanna M. Parkhill, Julian Langford, Paul R. Rycroft, Andrew N. Wren, Brendan W. Holden, Matthew T. G. Tucker, Alexander W. Maskell, Duncan J.. |
| author2_role |
author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Genome wide association study Pan-genome Recombination DAPC Virulence factors Population structure Haemophilus parasuis |
| topic |
Genome wide association study Pan-genome Recombination DAPC Virulence factors Population structure Haemophilus parasuis |
| description |
Haemophilus parasuis is the etiologic agent of Glässer's disease in pigs and causes devastating losses to the farming industry. Whilst some hyper-virulent isolates have been described, the relationship between genetics and disease outcome has been only partially established. In particular, there is weak correlation between serovar and disease phenotype. We sequenced the genomes of 212 isolates of H. parasuis and have used this to describe the pan-genome and to correlate this with clinical and carrier status, as well as with serotype. Recombination and population structure analyses identified five groups with very high rates of recombination, separated into two clades of H. parasuis with no signs of recombination between them. We used genome-wide association methods including discriminant analysis of principal components (DAPC) and generalised linear modelling (glm) to look for genetic determinants of this population partition, serovar and pathogenicity. We were able to identify genes from the accessory genome that were significantly associated with phenotypes such as potential serovar specific genes including capsule genes, and 48 putative virulence factors that were significantly different between the clinical and non-clinical isolates. We also show that the presence of many previously suggested virulence factors is not an appropriate marker of virulence. These genes will inform the generation of new molecular diagnostics and vaccines, and refinement of existing typing schemes and show the importance of the accessory genome of a diverse species when investigating the relationship between genotypes and phenotypes. The online version of this article (doi:10.1186/1471-2164-15-1179) contains supplementary material, which is available to authorized users. |
| publishDate |
2014 |
| dc.date.none.fl_str_mv |
2 2014-01-01 2014 2014-01-01 |
| dc.type.none.fl_str_mv |
Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://ddd.uab.cat/record/254630 https://dx.doi.org/urn:doi:10.1186/1471-2164-15-1179 |
| url |
https://ddd.uab.cat/record/254630 https://dx.doi.org/urn:doi:10.1186/1471-2164-15-1179 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf |
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reponame:Dipòsit Digital de Documents de la UAB instname:Universitat Autònoma de Barcelona |
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