Biological characterization and genome analysis of pathogenic Yersinia ruckeri causing enteric redmouth disease (ERM) in crucian carp (Carassius carassius)

Enteric redmouth disease (ERM) is a severe hemorrhagic bacterial infection that causes high mortality in kinds of fish. We isolated a dominant strain from diseased crucian carp, identified as Yersinia ruckeri, a member of Enterobacteriaceae, and confirmed this strain as the causative agent of the disease outbreak through morphological observation, histopathological examination, molecular diagnostic analyses and artificial infection. The results indicated that the isolated bacteria strain Yersinia ruckeri designated as QDH202303 (GenBank: CP177154) exhibited significant pathogenicity in crucian carp (Carassius carassius) and was the the primary cause of the disease outbreak. The LD50 value of Y. ruckeri was calculated as 3.3 × 104 CFU/fish. In the antibiotic susceptibility assay, the bacterial strain QDH202303 was resistant to 32 common antibiotics except polymyxin B, which showed broad-spectrum antibiotic resistance. Through whole-genome sequencing and sequence analysis, 7 resistance genes, 697 virulence factors were identified, which were associated with pathogenicity and broad-spectrum drug resistance. What's more, 13 genomic islands were identified, and three of them were related to the Type III secretion system, flagella, and yhlBA respectively. To the best of our knowledge, this is the first report of Y. ruckeri being identified as the causative agent of ERM disease in crucian carp. This study would provide valuable insights for the prevention and management of ERM diseases in aquaculture.