Genetic diversity of Flavobacterium psychrophilum isolated from rainbow trout in France: Predominance of a clonal complex

Flavobacterium psychrophilum is the causative agent of “bacterial cold water disease” and “rainbow trout fry syndrome” in salmonid farming worldwide. These diseases, especially rainbow trout fry syndrome, are among the main hazards for French aquaculture. In this study, a multilocus sequence typing approach (MLST) was used to evaluate the genetic diversity of this bacterium.Seven housekeeping genes in a set of 66 isolates were investigated. They were recently collected from rainbow trout during clinical episodes in French farms from the two main geographical areas of production. A total of 5808 bp of sequence were analyzed for each isolate and showed relatively low levels of gene (H = 0.4313) and nucleotide (π × 100 = 0.31%) diversities. MLST identified 15 sequence types (STs), of which 14 have never been described. eBURST analysis separated the 15 STs in one clonal complex of 8 genetically related STs (with ST2 as founder) and 7 singletons. Genetic diversity was largely due to recombination, as demonstrated by a pairwise homoplasy index (PHI = 5.35 × 10−9) significantly different from zero (p < 0.05). The evolution of standardized association index (IAS) (all isolates: 0.6088, p < 0.05; single representative of STs: 0.4567, p < 0.05; and clusters of STs: 0.084, p > 0.05), showed an epidemic structure of the population.These results emphasized the expansion of a limited number of dominant genetic variants in French clinical F. psychrophilum isolates from a single host species, with no geographic relationships.