Abstract
The bacterium Flavobacterium psychrophilum is a serious problem for salmonid farming worldwide. This study investigates by multilocus sequence typing (MLST) the population structure of this pathogen in Japan where it is also a major concern for ayu, a popular game fish related to salmoniforms. A total of 34 isolates collected across the country and 80 isolates sampled in a single model river by electrofishing were genotyped. The data accounting for 15 fish species allowed identifying 35 distinct sequence types (ST) in Japan. These ST are distinct from those reported elsewhere, except for some ST found in rainbow trout and coho salmon, two fish that have been the subject of intensive international trade. The pattern of polymorphism is, however, strikingly similar across geographical scales (model river, Japan, world) in terms of the fraction of molecular variance linked to the fish host (~50%) and of pairwise nucleotide diversity between ST (~5 Kbp-1). These observations go against the hypothesis of a recent introduction of F. psychrophilum in Japan. Two findings were made that are important for disease control: 1) at least two independent F. psychrophilum lineages infect ayu and 2) co-infections of the same individual fish by different strains occur.
Highlights
Diseases are an important problem in fish farming and control of bacterial pathogens relies mostly on repeated antibiotic treatments incompatible with the development of sustainable aquaculture [1]
The fish-pathogenic bacterium Flavobacterium psychrophilum is the causative agent of the “bacterial cold water disease” (BCWD) and the “rainbow trout fry syndrome”, two salmonid diseases that cause considerable losses in rainbow trout (Oncorhynchus mykiss) and coho salmon (Oncorhynchus kisutch) farming industries worldwide [2,3,4,5]
Yellow colonies were selected for identification as F. psychrophilum based on the Polymerase chain reaction (PCR) amplification of the 16S rRNA and gyrB genes [18,28,29] according to the guidelines of the council for the control of bacterial cold water disease of ayu (Japanese Ministry of Agriculture, Forestry and Fisheries)
Summary
Diseases are an important problem in fish farming and control of bacterial pathogens relies mostly on repeated antibiotic treatments incompatible with the development of sustainable aquaculture [1]. Many species beyond the ayu and farmed rainbow trout and coho salmon have been reported to harbor F. psychrophilum in Japan. These include migrating salmonids whose geographical ranges extend throughout the north-Pacific and more local species and subspecies. Following the publication of the complete genome sequence of a F. psychrophilum strain [25], a first Multilocus sequence typing (MLST) analysis was conducted on a set of 50 isolates collected from different fish species in different countries over the world [17] This initial study identified 33 different sequence types (ST), some of which could be grouped into clonal complexes (CC) associated with particular fish species, especially rainbow trout and coho salmon. We compare the patterns of polymorphism at the world, country and single model river levels
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