Comparative genome analysis reveals important genetic differences among serotype O1 and serotype O2 strains of Y. ruckeri and provides insights into host adaptation and virulence

Abstract

Despite the existence of a commercial vaccine routinely used to protect salmonids against Yersinia ruckeri, outbreaks still occur, mainly caused by nonmotile and lipase‐negative strains (serotype O1 biotype 2). Moreover, epizootics caused by other uncommon serotypes have also been reported. At the moment, one of the main concerns for the aquaculture industry is the expanding range of hosts of this pathogen and the emergence of new biotypes and serotypes causing mortality in fish farms and against which the vaccine cannot protect. The comparative analysis of the genome sequences of five Y. ruckeri strains (150, CSF007‐82, ATCC29473, Big Creek 74, and SC09) isolated from different hosts and classified into different serotypes revealed important genetic differences between the genomes analyzed. Thus, a clear genetic differentiation was found between serotype O1 and O2 strains. The presence of 99 unique genes in Big Creek 74 and 261 in SC09 could explain the adaptation of these strains to salmon and catfish, respectively. Finally, the absence of 21 genes in ATCC29473 which are present in the other four virulent strains could underpin the attenuation described for this strain. The study reveals important genetic differences among the genomes analyzed. Further investigation of the genes highlighted in this study could provide insights into the understanding of the virulence and niche adaptive mechanisms of Y. ruckeri.

The repeat structure of two paralogous genes, Yersinia ruckeri invasin (yrInv) and a “Y. ruckeri invasin-like molecule”, (yrIlm) sheds light on the evolution of adhesive capacities of a fish pathogen

“…ruckeri strains, especially between the serotype O1 and O2 strains (Cascales et al, 2017). Furthermore, a new Y. ruckeri serotype O8 was recently identified in Atlantic salmon in Scotland .…”

“…Among the unique proteins that are present only in SC09 is thymidylate synthase, which was previously shown to be linked to the intracellular growth of S. aureus and S. typhimurium (Kriegeskorte et al, 2014). Finally, the fact that the genome of ATCC29473 (type strain) lacks 21 genes that are involved mostly in virulence, could explain the attenuation of the strain (Cascales et al, 2017;Kriegeskorte et al, 2014).…”

“…It was suggested that the T4SS might be required for the pathogen's survival in fish macrophages . A recent comparative analysis of genome sequences of Y. ruckeri strains (150, CSF007-82, ATCC29473) showed that 268 genes were shared between them, and genes of the T4SS were present among them (Cascales et al, 2017).…”

Effects of siRNA silencing on the susceptibility of the fish cell line CHSE-214 to Yersinia ruckeri

“…Furthermore, several isolates of Y. ruckeri belonging to the O1 serotype also carry a cluster of fimbrial gene homologous to the STF cluster of S. typhimurium [10,11]. However, this cluster is absent from the ATCC 29473 type strain studied here [11].…”

“…Interestingly; while Y. ruckeri does not harbour a YadA equivalent, it is known to harbour two homologs of invasin: Y. ruckeri invasin (YrInv) and Y. ruckeri invasin-like molecule (YrIlm) [3]. Furthermore, several isolates of Y. ruckeri belonging to the O1 serotype also carry a cluster of fimbrial gene homologous to the STF cluster of S. typhimurium [10,11]. However, this cluster is absent from the ATCC 29473 type strain studied here [11].…”