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.

Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

“…This situation is in sharp contrast to that in F. psychrophilum (59,62,63), R. salmoninarium (61), and Y. ruckeri (60), for which the sequence data unambiguously revealed transcontinental dissemination linked to the international trade of broodfish and eggs. Furthermore, as a result of preferential dissemination routes or of adaptive niche specificity, the large clonal complexes detected in F. psychrophilum tended to be strongly associated with particular host fish species (59,62,64).…”

“…After Flavobacterium psychrophilum ( 59), Yersinia ruckeri (60), and Renibacterium salmoninarum (61), T. maritimum becomes the fourth species of fish-pathogenic bacteria for which sequence data are available for a significant number of strains. The niche of T. maritimum differs from that of the other three species, as it is the only marine bacterium with broad host range.…”

Complete Genome Sequence of the Fish Pathogen Flavobacterium branchiophilum

“…Intense gene transfer is suggested by the large number of genomic islands and by the presence of one plasmid; together with the accumulation of genomic rearrangements, gene transfer could have an important role in the diversification of the species. Indeed, Flavobacterium species are highly prone to homologous recombination (39,60) and represent the major recipients of natural gene transfer agents in the oceans (36).…”

Structure of Flavobacterium psychrophilum populations infecting farmed rainbow trout Oncorhynchus mykiss

“…Flavobacterium psychrophilum is considered genetically homogeneous as a species (Nicolas et al 2008), and apparent associations between closely related isolates and the rainbow trout host have been made (Chen et al 2008, Siekoula-Nguedia et al 2012). In our study, the F. psychrophilum isolates recovered from infected rainbow trout from 3 different fish farms were characterized by limited genetic variability.…”

“…The genotypic variability in Flavobacterium psychrophilum has previously been analyzed by random amplification of polymorphic DNA (RAPD; Chakroun et al 1997), restriction fragment length polymorphism of PCR products (PCR-RFLP; Izumi et al 2003), ribotyping (Cipriano et al 1996, Chakroun et al 1998, Dalsgaard & Madsen 2000, Madsen & Dalsgaard 2000, Madetoja et al 2002, polymorphism in 16s rRNA genes (Soule et al 2005a), reciprocal suppression subtractive hybridization by microarray analysis (Soule et al 2005b), and multilocus sequence typing (MLST; Nicolas et al 2008). Alone or in combination with other genotyping methods, plasmid profiling has also been used as a tool for genetic characterization of F. psychrophilum isolates (Lorenzen et al 1997, Chakroun et al 1998, Izumi & Aranishi 2004a, Kim et al 2010.…”