Genome Sequence of the Fish Pathogen Yersinia ruckeri SC09 Provides Insights into Niche Adaptation and Pathogenic Mechanism

Int J Mol Sci. 2016 Apr 14;17(4):557. doi: 10.3390/ijms17040557.


Yersinia ruckeri is the etiologic agent of enteric red mouth disease (ERM), a severe fish disease prevailing in worldwide aquaculture industries. Here we report for the first time the complete genome of Y. ruckeri (Yersinia ruckeri) SC09, a highly virulent strain isolated from Ictalurus punctatus with severe septicemia. SC09 possesses a single chromosome of 3,923,491 base pairs, which contains 3651 predicted protein coding sequences (CDS), 19 rRNA genes, and 79 tRNA genes. Among the CDS, we have identified a Ysa locus containing genes encoding all the components of a type III secretion system (T3SS). Comparative analysis suggest that SC09-Ysa share extensive similarity in sequence, gene content, and gene arrangement with Salmonella enterica pathogenicity island 1 (SPI1) and chromosome-encoded T3SS from Yersinia enterocolitica biotype 1B. Furthermore, phylogenetic analysis shown that SC09-Ysa and SPI1-T3SS belong on the same branch of the phylogenetic tree. These results suggest that SC09-Ysa and SPI1-T3SS appear to mediate biological function to adapt to specific hosts with a similar niche, and both of them are likely to facilitate the development of an intracellular niche. In addition, our analysis also indicated that a substantial part of the SC09 genome might contribute to adaption in the intestinal microenvironment, including a number of proteins associated with aerobic or anaerobic respiration, signal transduction, and various stress reactions. Genomic analysis of the bacterium offered insights into the pathogenic mechanism associated with intracellular infection and intestinal survivability, which constitutes an important first step in understanding the pathogenesis of Y. ruckeri.

Keywords: Yersinia ruckeri; niche adaptation; pathogenicity; type III secretion system; whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Chromosome Mapping
  • Fish Diseases / microbiology*
  • Fish Diseases / pathology
  • Genome, Bacterial
  • Genomic Islands
  • Ictaluridae / microbiology*
  • Multigene Family
  • Oncorhynchus mykiss / microbiology
  • Phylogeny
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • Signal Transduction
  • Type II Secretion Systems / genetics
  • Type II Secretion Systems / metabolism
  • Type III Secretion Systems / genetics
  • Type III Secretion Systems / metabolism
  • Yersinia Infections / microbiology
  • Yersinia Infections / veterinary*
  • Yersinia ruckeri / genetics*
  • Yersinia ruckeri / pathogenicity
  • Yersinia ruckeri / physiology


  • Bacterial Proteins
  • RNA, Bacterial
  • Type II Secretion Systems
  • Type III Secretion Systems