The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis
Howell, Kate J. (University of Cambridge. Department of Veterinary Medicine)
Weinert, Lucy A. (University of Cambridge. Department of Veterinary Medicine)
Chaudhuri, Roy R. (University of Sheffield. Department of Molecular Biology and Biotechnology)
Luan, Shi-Lu (University of Cambridge. Department of Veterinary Medicine)
Peters, Sarah E. (University of Cambridge. Department of Veterinary Medicine)
Corander, Jukka (University of Helsinki. Department of Mathematics and Statistics)
Harris, David (Wellcome Trust Sanger Institute (Regne Unit))
Angen, Øystein (Norwegian Veterinary Institute)
Aragon, Virginia (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal)
Bensaid, Albert (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal)
Williamson, Susanna M. (Animal Health and Veterinary Laboratories Agency)
Parkhill, Julian (Wellcome Trust Sanger Institute (Regne Unit))
Langford, Paul R. (Imperial College London. Department of Medicine, Section of Paediatrics)
Rycroft, Andrew N. (The Royal Veterinary College)
Wren, Brendan W. (London School of Hygiene and Tropical Medicine)
Holden, Matthew T. G. (University of St. Andrews. School of Medicine)
Tucker, Alexander W. (University of Cambridge. Department of Veterinary Medicine)
Maskell, Duncan J.. (University of Cambridge. Department of Veterinary Medicine)

Data:	2014
Resum:	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.
Drets:	Aquest 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.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Genome wide association study ; Pan-genome ; Recombination ; DAPC ; Virulence factors ; Population structure ; Haemophilus parasuis
Publicat a:	BMC genomics, Vol. 15 (december 2014) , ISSN 1471-2164

DOI: 10.1186/1471-2164-15-1179
PMID: 25539682

18 p, 1.9 MB

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Documents de recerca > Documents dels grups de recerca de la UAB > Centres i grups de recerca (producció científica) > Ciències de la salut i biociències > Centre de Recerca en Sanitat Animal (CReSA-IRTA)
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