Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa

Abstract

BackgroundWinter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M. viscosa strains. Matches between M. viscosa clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) were analysed to correlate CRISPR-Cas with adaptive immunity against MGEs.ResultsThe comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follow the phylogenetic lineages. A subset of the spacer content match prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid-like element distribution were reflected in the content of the CRISPR-spacer profiles.ConclusionsOur data suggests that CRISPR-Cas mediated interactions with MGEs impact genome properties among M. viscosa, and that patterns in spacer and MGE distributions are linked to strain relationships.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3693-7) contains supplementary material, which is available to authorized users.

Moritella viscosa in lumpfish (Cyclopterus lumpus) and Atlantic salmon (Salmo salar)

“…However, analysis of whole M. viscosa genomes by Karlsen et al. (Karlsen, Hjerde et al., ; Karlsen, Thorarinsson et al., ) indicates that variability in the gyrB gene may not be sufficient to define sublineages.…”

“…To conclude, it remains to be examined whether lumpfish can transmit M. viscosa to salmon in cohabitation and whether vaccinating lumpfish can prevent transmission, given that lumpfish isolates are a component of the vaccine. However, vaccination of lumpfish against M. viscosa has not elicited high antibody titres against the bacterium (Erkinharju et al., ), although antibody levels may not be a good indicator of protection (Karlsen, Hjerde et al., ; Karlsen, Thorarinsson et al., ). Until it has been established whether vaccination can effectively protect lumpfish against M. viscosa , rigorous screening of lumpfish for subclinical infection and screening of dead salmon removed from sea pens may be the most effective preventative measure.…”

“…Comparison of the gyrB sequences to data published by Grove et al (Grove et al, 2010) indicates that all Icelandic M. viscosa isolates are "variant type" (Figure 1, upper branch), which is a genetically different cluster from the species type strain (NCIMB 13548, not shown). However, analysis of whole M. viscosa genomes by Karlsen et al (Karlsen, Hjerde et al, 2017;Karlsen, Thorarinsson et al, 2017) indicates that variability in the gyrB gene may not be sufficient to define sublineages.…”

“…Karlsen et al. sequenced the genomes of twelve M. viscosa from four different fish species, including one isolate from lumpfish (Karlsen, Hjerde, Klemetsen, & Willassen, ; Karlsen, Thorarinsson, Wallace, Salonius, & Midtlyng, ). Based on the data, the lumpfish isolate grouped with a cod isolate, but the authors could not associate subgroups with the host type.…”

“…While sequencing of the 16S rRNA gene is typically used for identification of M. viscosa, the gyrase B (gyrB) gene is more variable and has been used to distinguish subtypes of M. viscosa (Grove et al, 2010). Karlsen et al sequenced the genomes of twelve M. viscosa from four different fish species, including one isolate from lumpfish (Karlsen, Hjerde, Klemetsen, & Willassen, 2017;Karlsen, Thorarinsson, Wallace, Salonius, & Midtlyng, 2017). Based on the data, the lumpfish isolate grouped with a cod isolate, but the authors could not associate subgroups with the host type.…”