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Applied and Environmental Microbiology, June 2008, p. 3702-3709, Vol. 74, No. 12
0099-2240/08/$08.00+0     doi:10.1128/AEM.00244-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Population Structure of the Fish-Pathogenic Bacterium Flavobacterium psychrophilum

Pierre Nicolas,^1* Stanislas Mondot,^2, Guillaume Achaz,^3,4 Catherine Bouchenot,² Jean-François Bernardet,² and Eric Duchaud²

INRA, Mathématique Informatique et Génome UR1077, F-78350 Jouy-en-Josas, France,¹ INRA, Virologie et Immunologie Moléculaires UR892, F-78350 Jouy-en-Josas, France,² Université Pierre et Marie Curie-Paris 6, Atelier de Bioinformatique, F-75005 Paris, France,³ Université Pierre et Marie Curie-Paris 6, Systématique Adaptation Evolution UMR7138, F-75005 Paris, France⁴

Received 28 January 2008/ Accepted 14 April 2008

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.

Published ahead of print on 18 April 2008.

Present address: INRA, Ecologie et de Physiologie du Système Digestif UR910, F-78350 Jouy-en-Josas, France.