Delineating the key virulence factors and intraspecies divergence of via whole-genome sequencing.

is one of the major pathogens in aquaculture. To identify the key virulence factors affecting pathogenesis of towards fish, we conducted a field investigation for three representative fish farms infected with . Multilocus sequence typing (MLST) and whole-genome sequencing were conducted to delineate the phylogenetic relationship and genetic divergence of . A total of 25 strains were isolated from the diseased fish and groundwater and were subtyped into 12 sequence types by MLST. Five virulence genes, , , , , and , were variably presented in the sequenced strains. The virulence gene profiles strongly correlated with the distinct pathogenicity of strains, with a strain harboring all five genes exhibiting the highest virulence towards fish. Phenotype assay confirmed that reduced virulence correlated with decreased motility and biofilm formation ability. Additionally, three types of type VI secretion system, namely T6SS1, T6SS2, and T6SS3, were identified in strains, which can be classified into six, four, and 12 subtypes, respectively. In conclusion, the results indicated that the virulence level of is mainly determined by the above virulence genes, which may play vital roles in environmental adaptation for