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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #397249

Research Project: Improving Salmonid Health through Breeding, Vaccination and Microbiome Modulation

Location: Cool and Cold Water Aquaculture Research

Title: Pan-genome survey of the fish pathogen Yersinia ruckeri links accessory- and amplified genes to virulence

item RIBORG, ANDREAS - Norwegian Veterinary Institute
item GULLA, SNORRE - Norwegian Veterinary Institute
item COLQUHOUN, DUNCAN - Norwegian Veterinary Institute
item ZEYL FISKEBECK, EVE - Norwegian Veterinary Institute
item RYDER, DAVID - Centre For Environment, Fisheries And Aquaculture Science (CEFAS)
item VERNER-JEFFREYS, DAVID - Centre For Environment, Fisheries And Aquaculture Science (CEFAS)
item Welch, Timothy - Tim

Submitted to: PLoS Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2023
Publication Date: 5/11/2023
Citation: Riborg, A., Gulla, S., Colquhoun, D.J., Zeyl Fiskebeck, E., Ryder, D., Verner-Jeffreys, D., Welch, T.J. 2023. Pan-genome survey of the fish pathogen Yersinia ruckeri links accessory- and amplified genes to virulence. PLoS Pathogens. (18)5:e0285257.

Interpretive Summary: Yersinia ruckeri is the causative agent of enteric redmouth disease in aquaculture, a bacterial disease primarily affecting salmonid fish. Serious outbreaks in aquaculture are generally caused by a small number of disease-causing strains, while relatively harmless strains are known to exist in the environment. While many genes necessary for causing disease in Y. ruckeri (virulence genes) have been identified and studied, the relationship between their presence and severe disease remains poorly understood. In the present work, a broad study of genomic sequences across Y. ruckeri strains of varying disease severity revealed a number of previously described virulence genes as present in all strains. Others were also present in many of the harmless strains. Although a number of genetic determinants were overrepresented in disease-causing lineages, only the presence of one gene correlated fully and exclusively with a disease phenotype. The identification of genes that are unique to disease-causing lineages will inform improved disease diagnostic strategies that can resolve between strains that are harmless and strains that have the potential to cause severe disease.

Technical Abstract: While both virulent and putatively avirulent Yersinia ruckeri strains exist in aquaculture environments, the relationship between the distribution of virulence-associated factors and de facto pathogenicity in fish remains poorly understood. Pan-genome analysis of 18 complete genomes, representing established virulent and putatively avirulent lineages of Y. ruckeri, revealed the presence of a number of accessory genetic determinants. Further investigation of 68 draft genome assemblies revealed that the distribution of certain putative virulence factors correlated well with virulence and host-specificity. The inverse-autotransporter invasin yrIlm was, however, the only gene present in all virulent strains, while absent in lineages regarded as avirulent. Strains known to be associated with significant mortalities in salmonid aquaculture display a combination of serotype O1-LPS and yrIlm, with the well-documented highly virulent lineages, represented by MLVA clonal complexes 1 and 2, displaying duplication of the yrIlm locus. Duplication of the yrIlm locus was further found to have evolved over time in clonal complex 1, where some modern, highly virulent isolates display up to three copies.