Comparative Genomic Analyses of Flavobacterium psychrophilum Isolates Reveals New Putative Genetic Determinants of Virulence Traits

Daniel Castillo,Jóhanna Jørgensen,Lone Madsen,Tom Wiklund,Inger Dalsgaard,Mathias Middelboe,Krister Sundell,Valentina L Donati

doi:10.3390/microorganisms9081658

Abstract

The fish pathogen Flavobacterium psychrophilum is currently one of the main pathogenic bacteria hampering the productivity of salmonid farming worldwide. Although putative virulence determinants have been identified, the genetic basis for variation in virulence of F. psychrophilum is not fully understood. In this study, we analyzed whole-genome sequences of a collection of 25 F. psychrophilum isolates from Baltic Sea countries and compared genomic information with a previous determination of their virulence in juvenile rainbow trout. The results revealed a conserved population of F. psychrophilum that were consistently present across the Baltic Sea countries, with no clear association between genomic repertoire, phylogenomic, or gene distribution and virulence traits. However, analysis of the entire genome of four F. psychrophilum isolates by hybrid assembly provided an unprecedented resolution for discriminating even highly related isolates. The results showed that isolates with different virulence phenotypes harbored genetic variances on a number of consecutive leucine-rich repeat (LRR) proteins, repetitive motifs in gliding motility-associated protein, and the insertion of transposable elements into intergenic and genic regions. Thus, these findings provide novel insights into the genetic variation of these elements and their putative role in the modulation of F. psychrophilum virulence.

Highlights

Flavobacterium psychrophilum is a yellow-pigmented, Gram-negative fish pathogenic bacterium with a global distribution in freshwater aquaculture, and causing “bacterial cold water disease” (BCWD) and “rainbow trout fry syndrome” (RTFS) [1]
The results obtained in this study showed that in F. psychrophilum the accessory gene content was not linked with virulence traits by LD50 (Figure 1), interesting genes were found in a genomic island of 320 kb in the moderately virulent F. psychrophilum isolate FPS-R7
Diverse putative virulence-related genes have been identified in genomic sequences of F. psychrophilum, the role played by other genetic factors in the development of BCWS and RTFS diseases is still poorly understood [3,11]

Summary

Introduction

Flavobacterium psychrophilum is a yellow-pigmented, Gram-negative fish pathogenic bacterium with a global distribution in freshwater aquaculture, and causing “bacterial cold water disease” (BCWD) and “rainbow trout fry syndrome” (RTFS) [1]. The disease results in high rates of fry mortality, increased tendency for other infections, and high costs of treatment with antibiotics; causing important economic losses for salmonid aquaculture worldwide [2]. A diverse array of visible phenotypic alterations are attributable to F. psychrophilum infection, including necrotic lesions, partial dark skin coloration, exophthalmia, anemia, ascites, and vertebral deformities of the fish [1,2]. These signs have been related to the presence of extracellular proteases [3], adhesion or biofilm formation [4], hemolysis [5], and secreted systems [6,7]. The initial isolation of F. psychrophilum was reported in the USA in the 1940s [1]; since F. psychrophilum isolates have been obtained from all salmonid producing countries, including European nations [8,9,10].

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Results

Discussion

Conclusion