Comparative genomic analysis of the novel strain Vibrio cidicii VC01, isolated from China.

Vibrio cidicii is an opportunistic pathogen that is widely distributed in the environment worldwide. Using whole-genome sequencing (WGS), we investigated the genetic characteristics of V. cidicii isolated from the seawater (named as V. cidicii VC01) by the Chinese Center for Disease Control and Prevention in Nantong, China. VC01 comprised two circular chromosomes, containing 4,013 potential coding sequences and 151 RNA genes. A phylogenetic tree constructed from the 16S rRNA genes of Vibrio spp. indicated that V. cidicii strains were closely related to V. navarrensis strains. The phylogenetic tree of single nucleotide polymorphisms revealed that 19 V. cidicii strains, including 18 V. cidicii strains from the National Center for Biotechnology Information database and VC01, were divided into three genotypes with VC01 belonging to genotype 2. Based on the genetic screening of virulence factors, the 19 strains were classified into nine functional categories, and the differences between strains were mainly in adherence and immune modulation. All V. cidicii strains carried six antimicrobial resistance genes (AMRs), while VC01 carried two additional AMRs (dfrA3 and qnrVC6). We defined five V. cidicii O-genotypes (VCOg, named VCOg1-VCOg5) based on analyses of the O-antigen biosynthesis gene clusters (O-AGCs). The O-AGCs genotype of V. cidicii VC01 was VCOg4. Based on WGS, we found that VC01 carried a Tn7-like transposon with a type I restriction-modification system. Through comparative analysis, we first revealed the O-AGCs diversity in V. cidicii strains and the unique strain VC01 carrying a Tn7-like transposon with a type I restriction-modification system. IMPORTANCE: Vibrio cidicii strains are opportunistic pathogens causing bacteremia in humans and can be multidrug-resistant. Since few studies report on Vibrio cidicii strains, there is a lack of knowledge of the genetic diversity, presence of antimicrobial resistance genes, and virulence factors in V. cidicii strains. This study revealed the genomic features, phylogeny, and diversity of V. cidicii strains, highlighting five O-antigen biosynthesis gene cluster genotypes in V. cidicii strains and a Tn7-like transposon carrying a type Ⅰ restriction-modification in VC01. These findings provide new insights into the genetic diversity and antimicrobial potential of V. cidicii strains.