Dataset Information

Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).

ABSTRACT: Flavobacterium psychrophilum is the causative agent of bacterial cold water disease and rainbow trout fry mortality syndrome in salmonid fishes and is associated with significant losses in the aquaculture industry. The virulence factors and molecular mechanisms of pathogenesis of F. psychrophilum are poorly understood. Moreover, at the present time, there are no effective vaccines and control using antimicrobial agents is problematic due to growing antimicrobial resistance and the fact that sick fish don't eat. In the hopes of identifying vaccine and therapeutic targets, we sequenced the genome of the type strain ATCC 49418 which was isolated from the kidney of a Coho salmon (Oncorhychus kisutch) in Washington State (U.S.A.) in 1989. The genome is 2,715,909 bp with a G+C content of 32.75%. It contains 6 rRNA operons, 49 tRNA genes, and is predicted to encode 2,329 proteins.

SUBMITTER: Wu AK

PROVIDER: S-EPMC4322650 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).

Wu Anson Kk AK Kropinski Andrew M AM Lumsden John S JS Dixon Brian B MacInnes Janet I JI

Standards in genomic sciences 20150121

Flavobacterium psychrophilum is the causative agent of bacterial cold water disease and rainbow trout fry mortality syndrome in salmonid fishes and is associated with significant losses in the aquaculture industry. The virulence factors and molecular mechanisms of pathogenesis of F. psychrophilum are poorly understood. Moreover, at the present time, there are no effective vaccines and control using antimicrobial agents is problematic due to growing antimicrobial resistance and the fact that sick ...[more]

PMID: 25685258

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Project description:Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout (Oncorhynchus mykiss) worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless "open" according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of F. psychrophilum, a particular attention was also paid to plasmids. Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities.

Project description:Hydrolytic extracellular enzymes degrading host tissues potentially play a role in bacterial pathogenesis. Flavobacterium psychrophilum is an important bacterial pathogen of salmonid fish reared in freshwater throughout the world. Diversity among isolates has been described at the phenotypic, serological, and genomic levels, but the links between these various traits remain poorly understood. Using a genome-wide association study, we identified a gene encoding a novel elastinolytic enzyme in F. psychrophilum To formally demonstrate enzymatic activity, this gene (FP0506 from strain JIP 02/86) was expressed in the elastinolysis-deficient strain OSU THCO2-90, resulting in proficient elastin-degrading cells. The encoded protein is predicted to be a cell-surface-exposed lipoprotein with no homology to previously reported elastases. FP0506 might belong to the zincin tribe and gluzincin clan of metalloproteases, and this new elastase-encoding gene seems to be present only in some members of the family Flavobacteriaceae IMPORTANCE Elastin is an important proteinaceous component of vertebrate connective tissues (e.g., blood vessels, lung, and skin), to which it confers elasticity. Elastases have been identified in a number of pathogenic bacteria. They are thought to be required for tissue penetration and dissemination, acting as "spreading factors." Flavobacterium psychrophilum is a devastating bacterial pathogen of salmonid fish (salmon and trout) that is responsible for severe economic losses worldwide. This pathogen displays strong proteolytic activities. Using a variety of techniques, including genome comparisons, we identified a gene encoding a novel elastase in F. psychrophilum The encoded protein is predicted to be a cell-surface-exposed lipoprotein with no homology to previously reported elastases. In addition, this elastase likely belongs to a new family of proteases that seems to be present only in some members of this important group of bacteria.

Dataset Information

Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).

Publications

Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).

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