title: Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum.
abstract: Flavobacterium psychrophilum is currently one of the main bacterial pathogens 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 polymorphisms 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, originating from 10 different host fish species and four continents. The nucleotide diversity between pairs of sequences amounted to fewer than four differences per kilobase on average, corresponding to a particularly low level of diversity, possibly indicative of a small effective-population size. The recombination rate, however, seemed remarkably high, and as a consequence, most of the isolates harbored unique combinations of alleles (33 distinct sequence types were resolved). The analysis also showed the existence of several clonal complexes with worldwide geographic distribution but marked association with 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 reflect the spread of a few clonal complexes. As a resource for future epidemiological surveys, a multilocus sequence typing website based on seven highly informative loci is available.
authors.affiliation: INRA, Mathématique Informatique et Génome UR1077, F-78350 Jouy-en-Josas, France. pierre.nicolas@jouy.inra.fr
authors.forename: Pierre
authors.initials: P
authors.lastname: Nicolas
authors.forename: Stanislas
authors.initials: S
authors.lastname: Mondot
authors.forename: Guillaume
authors.initials: G
authors.lastname: Achaz
authors.forename: Catherine
authors.initials: C
authors.lastname: Bouchenot
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Bernardet
authors.forename: Eric
authors.initials: E
authors.lastname: Duchaud
mesh_terms: D000483:Alleles; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005393:Fish Diseases / Q000382:microbiology*; D045826:Flavobacteriaceae Infections / Q000382:microbiology / Q000662:veterinary*; D005417:Flavobacterium / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D005838:Genotype; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial