Multiple-locus, variable number of tandem repeat analysis (MLVA) of the fish-pathogen Francisella noatunensis

Seven polymorphic VNTR loci were identified in the preliminary genome sequence of F. noatunensis ssp. noatunensis GM2212 isolate. These VNTR-loci were sequenced in F. noatunensis isolates collected from Atlantic cod (Gadus morhua) from Norway (n = 21), Three-line grunt (Parapristipoma trilineatum) from Japan (n = 1), Tilapia (Oreochromis spp.) from Indonesia (n = 3) and Atlantic salmon (Salmo salar) from Chile (n = 1). The Norwegian isolates presented in this study show both nine allelic profiles and clades, and that the majority of the farmed isolates belong in two clades only, while the allelic profiles from wild cod are unique.VNTRs can be used to separate isolates belonging to both subspecies of F. noatunensis. Low allelic diversity in F. noatunensis isolates from outbreaks in cod culture compared to isolates wild cod, indicate that transmission of these isolates may be a result of human activity. The sequence based MLVA system presented in this study should provide a good starting point for further development of a genotyping system that can be used in studies of epizootics and disease management of francisellosis.The intensive culturing of fish in artificially high population densities facilitates disease outbreaks [1,2]. Standard protocols for traditional fish health management, controlling and preventing diseases, have focused on vaccines, operational prophylactic measures and oral treatment using therapeutic agents [3]. However, in those cases where vaccines or treatments are not available, understanding the epizootiology becomes the key to prevent outbreaks and pathogen dispersal [1]. Using molecular tools for strain typing of pathogens, combined with biological and ecological knowledge of both the pathogen and the host, is a prerequisite in creating an epizootiological understanding which can be applied in management of diseases in both wild and cultured populations.Historically, the Atlantic cod (Gadus morhua) has been an important marine resource in Nor