Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum

Abstract

Flavobacterium psychrophilum is a fish pathogen in salmonid aquaculture worldwide that causes cold water disease (CWD) and rainbow trout fry syndrome (RTFS). Comparative genome analyses of 11 F. psychrophilum isolates representing temporally and geographically distant populations were used to describe the F. psychrophilum pan-genome and to examine virulence factors, prophages, CRISPR arrays, and genomic islands present in the genomes. Analysis of the genomic DNA sequences were complemented with selected phenotypic characteristics of the strains. The pan genome analysis showed that F. psychrophilum could hold at least 3373 genes, while the core genome contained 1743 genes. On average, 67 new genes were detected for every new genome added to the analysis, indicating that F. psychrophilum possesses an open pan genome. The putative virulence factors were equally distributed among isolates, independent of geographic location, year of isolation and source of isolates. Only one prophage-related sequence was found which corresponded to the previously described prophage 6H, and appeared in 5 out of 11 isolates. CRISPR array analysis revealed two different loci with dissimilar spacer content, which only matched one sequence in the database, the temperate bacteriophage 6H. Genomic Islands (GIs) were identified in F. psychrophilum isolates 950106-1/1 and CSF 259–93, associated with toxins and antibiotic resistance. Finally, phenotypic characterization revealed a high degree of similarity among the strains with respect to biofilm formation and secretion of extracellular enzymes. Global scale dispersion of virulence factors in the genomes and the abilities for biofilm formation, hemolytic activity and secretion of extracellular enzymes among the strains suggested that F. psychrophilum isolates have a similar mode of action on adhesion, colonization and destruction of fish tissues across large spatial and temporal scales of occurrence. Overall, the genomic characterization and phenotypic properties may provide new insights to the mechanisms of pathogenicity in F. psychrophilum.

The Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation

“…Similarly, Touchon et al reported that there were no incomplete prophage elements in F. branchiophilum FL-15 (Touchon et al, 2011 ). This may be partially explained due to the presence of multiple CRISPR loci in F. psychrophilum (1~2 loci) (Castillo et al, 2016 ), F. columnare (at least 3 loci) (Kayansamruaj et al, 2017 ), and F. branchiophilum FL-15 (at least 3 loci) (Touchon et al, 2011 ; Barrangou and Marraffini, 2014 ; van Houte et al, 2016 ). It is interesting that we did not detect any CRISPR elements in F. spartansii T16 T , which may coincide with presence of prophages, genomic islands, and conjugative transposons in its genome.…”

“…(McBride et al, 2009 ; Barbier et al, 2012 ; Kumru et al, 2017 ) and additional genome sequence data are now available for multiple strains of the fish pathogens F. columnare (Bartelme et al, 2016 ; Zhang et al, 2016 ), F. psychrophilum (Wiens et al, 2014 ; Wu et al, 2015 ), and F. branchiophilum (Touchon et al, 2011 ). These studies have revealed some of the processes by which flavobacterial fish pathogens are believed to colonize, attack, and survive within fish hosts (Duchaud et al, 2007 ; Castillo et al, 2016 ), as well as how some of the molecular mechanisms vary amongst strains (Wiens et al, 2014 ; Wu et al, 2015 ; Bartelme et al, 2016 ; Zhang et al, 2016 ).…”

Large-Scale Analysis of Flavobacterium psychrophilum Multilocus Sequence Typing Genotypes Recovered from North American Salmonids Indicates that both Newly Identified and Recurrent Clonal Complexes Are Associated with Disease

“…STs that did not form part of a CC were referred to as singletons. All isolates within the publicly accessible MLST database for F. psychrophilum (n ϭ 1,097; https://pubmlst.org/ fpsychrophilum/) (15), including all previously typed isolates from North America (n ϭ 107) (7,13,39), along with the 314 isolates of this study, were included in the eBURST v3 (37,38) analysis.…”

Different Phenotypes of Mature Biofilm in Flavobacterium psychrophilum Share a Potential for Virulence That Differs from Planktonic State

“…Castillo et al (2016) recently reported that F. psychrophilum harbors at least 3373 genes and a core genome minimum of 1743 genes, with putative virulence factors uniformly distributed among 11 isolates from different sources and locations (Castillo et al, 2016). Remarkably, all of these isolates show similar capacities to form biofilms, with implications for their virulence and pathogenicity.…”