Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum

INRA, Mathématique Informatique et Génome UR1077, F-78350 Jouy-en-Josas, France; INRA, Virologie et Immunologie Moléculaires UR892, F-78350 Jouy-en-Josas, France; Université Pierre et Marie Curie-Paris 6, Atelier de Bioinformatique, F-75005 Paris, France; Université Pierre et Marie Curie-Paris 6, Systématique Adaptation Evolution UMR7138, F-75005 Paris, France

^* To whom correspondence should be addressed. Email: pierre.nicolas{at}jouy.inra.fr.

	Abstract

Flavobacterium psychrophilum is currently one of the main bacterial pathogen hampering the productivity of salmonid farming worldwide and its control mainly relies on antibiotic treatments. To better understand the population structure of this bacterium and its mode of evolution, we have examined the nucleotide polymorphism at 11 protein coding loci of the core genome in a set of 50 isolates. These isolates were selected to represent the broadest possible diversity, including ten different host fish species and four continents. Nucleotide diversity between pairs of sequences averaged to less than 4 differences per kilobase, corresponding to a particularly low diversity possibly indicative of a small effective population size. Recombination rate seemed, however, remarkably high and, as a consequence, most of the isolates harboured unique combination of alleles (33 distinct sequence types resolved). The analysis also showed the existence of several clonal complexes with worldwide geographic distribution but marked association to particular fish species. Such an association could reflect preferential routes of transmission and/or adaptive niche specialization. The analysis provided no clues that the initial range of the bacterium was originally limited to North-America. Instead, the historical record of the expansion of the pathogen may rather reflect the spread of a few clonal complexes. As a resource for future epidemiological surveys, a multi-locus sequence typing website based on seven highly informative loci is made available.