Genome Sequence of the Fish Pathogen Renibacterium salmoninarum Suggests Reductive Evolution away from an Environmental Arthrobacter Ancestor

Abstract

Renibacterium salmoninarum is the causative agent of bacterial kidney disease and a significant threat to healthy and sustainable production of salmonid fish worldwide. This pathogen is difficult to culture in vitro, genetic manipulation is challenging, and current therapies and preventative strategies are only marginally effective in preventing disease. The complete genome of R. salmoninarum ATCC 33209 was sequenced and shown to be a 3,155,250-bp circular chromosome that is predicted to contain 3,507 open-reading frames (ORFs). A total of 80 copies of three different insertion sequence elements are interspersed throughout the genome. Approximately 21% of the predicted ORFs have been inactivated via frameshifts, point mutations, insertion sequences, and putative deletions. The R. salmoninarum genome has extended regions of synteny to the Arthrobacter sp. strain FB24 and Arthrobacter aurescens TC1 genomes, but it is approximately 1.9 Mb smaller than both Arthrobacter genomes and has a lower G؉C content, suggesting that significant genome reduction has occurred since divergence from the last common ancestor. A limited set of putative virulence factors appear to have been acquired via horizontal transmission after divergence of the species; these factors include capsular polysaccharides, heme sequestration molecules, and the major secreted cell surface antigen p57 (also known as major soluble antigen). Examination of the genome revealed a number of ORFs homologous to antibiotic resistance genes, including genes encoding ␤-lactamases, efflux proteins, macrolide glycosyltransferases, and rRNA methyltransferases. The genome sequence provides new insights into R. salmoninarum evolution and may facilitate identification of chemotherapeutic targets and vaccine candidates that can be used for prevention and treatment of infections in cultured salmonids.

Pathological and immunological responses associated with differential survival of Chinook salmon following Renibacterium salmoninarum challenge

“…Avirulent and virulent strains of R. salmoninarum increased serum nitrate (functional measure of iNOS) in trout, with the highest nitrate response observed in fish that received the virulent strain (MT1729) and suffered the highest mortality (Campos-Perez et al 2000). The R. salmoninarum genome possesses at least 2 candidate genes that may be involved in sensing and resisting nitrogen radicals (Wiens et al 2008). The finding that the Green River stock had higher iNOS expression, even after accounting for the effect of bacterial load, suggests the possibility that higher nitric oxide production may have contributed to greater host cell collateral damage, leading to greater pathology.…”

Antibacterial Drugs in Fish Farms: Application and Its Effects

“…A serious disease of freshwater and seawater fish, farmed and wild salmonids, that results in an acute to chronic systemic granulomatous disease. Renibacterium salmoninarum is a Gram-positive diplococcus that grows best at 15-18°C, is causative agent of BKD and a significant threat to the healthy and sustainable production of salmonid fish worldwide (Wiens et al, 2008).…”

Renibacterium salmoninarum p57 antigenic variation is restricted in geographic distribution and correlated with genomic markers

“…The high prevalence of strains containing msa3 and the previous correlation with increased virulence suggests that diagnostic assays identifying this variant may have relevance, particularly for regions outside of North America that are negative for this variant. The presence of variable hybridization intensity in Southern blots indicates that msa3 likely resides on a low-copy number extra- Rhodes et al 2000, Wiens et al 2008). However, further DNA sequence and transcriptional analyses are needed to resolve the origin and relationship of the putative third msa gene to the msa1 and msa2 genes, and whether msa3 is functionally active or a pseudogene.…”

“…In this locus, Renibacterium salmoninarum strains have been reported to exhibit 2 different size variants, designated TR1 and TR2, that differ by a 51 bp exact repeat . The precise location of the ETR-A locus was investigated by examination of the whole genome sequence of the ATCC 33209 strain (Wiens et al 2008). A basic local alignment search tool (BLASTn) search using the 2 primer sequences identified locus ID RSal33209_ 2187, which is a 2865 bp open reading frame encoding a predicted protein of 955 amino acids assigned GenBank protein accession number YP_001625333.…”

“…These include using randomly amplified polymorphic DNA and rRNA intergenic spacer sequences (Grayson et al 1999), the ETR-A loci , and IS994 profiles (Rhodes et al 2000. The availability of the complete genome sequence of the ATCC 33209 strain (GenBank accession number NC_010168) now provides a starting point for understanding the molecular basis of some of these differences (Wiens et al 2008). In the present study, we identified the ETR as part of an open reading frame, designated RSal33209_2187, encoding a 955 aa protein with an unknown function.…”