Abstract
BackgroundSince Francisella noatunensis was first isolated from cultured Atlantic cod in 2004, it has emerged as a global fish pathogen causing disease in both warm and cold water species. Outbreaks of francisellosis occur in several important cultured fish species making a correct management of this disease a matter of major importance. Currently there are no vaccines or treatments available. A strain typing system for use in studies of F. noatunensis epizootics would be an important tool for disease management. However, the high genetic similarity within the Francisella spp. makes strain typing difficult, but such typing of the related human pathogen Francisella tullarensis has been performed successfully by targeting loci with higher genetic variation than the traditional signature sequences. These loci are known as Variable Numbers of Tandem Repeat (VNTR). The aim of this study is to identify possible useful VNTRs in the genome of F. noatunensis.ResultsSeven 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.ConclusionsVNTRs 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.
Highlights
Since Francisella noatunensis was first isolated from cultured Atlantic cod in 2004, it has emerged as a global fish pathogen causing disease in both warm and cold water species
Among the F. philomiragia isolates most allele variation was seen in Variable Numbers of Tandem Repeat (VNTR)-4, whereas no variations were detected in sequences from VNTR-2 and -6
VNTR-5 and -1 were not amplified from DSM 7535, but a blastn search was performed using these VNTR sequences obtained from F. noatunensis ssp. noatunensis GM2212 isolate
Summary
Since Francisella noatunensis was first isolated from cultured Atlantic cod in 2004, it has emerged as a global fish pathogen causing disease in both warm and cold water species. 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] In those cases where vaccines or treatments are not available, understanding the epizootiology becomes the key to prevent outbreaks and pathogen dispersal [1]. The Atlantic cod (Gadus morhua) has been an important marine resource in Norway, occurring naturally both as migratory and stationary populations [4,5,6]. These populations are divided into coastal and oceanic populations, based on phenotypic and genotypic traits. The oceanic and some of the coastal populations will, at certain times of the year, be present in at the same locations
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