Complete genome sequence of Vibrio mimicus strain SCCF01 with potential application in fish vaccine development

Vibrio mimicus strain SCCF01 was isolated from the yellow catfish (Pelteobagrus fulvidraco) during a mass mortality event at an aquaculture facility. We sequenced the genome of strain SCCF01, then predicted possible effective targets for subunit vaccine and identified possible virulence genes for live attenuated vaccine. The genome of SCCF01 consists of 2 circular chromosomes of 3,213,040 and 1,272,975 bp with G+C content of 46.61% and 45.88%, respectively. Subcellular localization, number of transmembrane helices and adhesion probability were predicted by Vaxign programs. Several candidate virulence genes were identified using the Virulence Factors Database. The genomic information presented herein will be useful for future studies investigating the pathogenesis of V. mimicus and with vaccine development. Vibrio mimicus is an enteric pathogen that is widely distributed in aquatic environments that can infect and cause disease in fish. Additionally, the pathogen is zoonotic and can cause bacterial gastroenteritis and food poisoning in humans if infected fish are consumed. Hence, understanding the pathogenesis of V. mimicus and developing a vaccine to treat infected fish hosts is an important research direction. In this study, we revived V. mimicus strain SCCF01 from the farmed yellow catfish (Pelteobagrus fulvidraco) in Sichuan Province, China, during a mass mortality event. Our objectives were to: (1) characterize the SCCF01 genome, (2) predict possible effective targets for subunit vaccine, (3) identify possible virulence genes that could lead to development of attenuated V. mimicus for vaccine development, and (4) identify the ability of colonization and adhesion of V. mimicus infection in yellow catfish. The whole-genome sequence of SCCF01 strain was determined with single molecule real-time (SMRT) sequencing platform PacBio RS II. Single SMRT cells produced 35,089 reads for 306,431,068 bases (N50 size 12,135 bp and mean read length 8,732 bp). Subsequently, the sequence reads were assembled using the PacBio SMRT Analysis (ver. 2.3.0) with default options. Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The rRNA/tRNA genes were identified by Barrnap version 0.6 (www.vicbioinformatics.com/software.barrnap.shtml) and tRNAscan-SE, respectively. The annotated genome was performed with the software Vaxign to further analyze subcellular localization, number of transmembrane helices and adhesion probability. In addition, possible virulence genes in SCCF01 were identified by Virulence Factors Database and software BLASTp. Bacterial levels of yellow catfish challenged with SCCF01 via water bath immersion were measured using qPCR. The entire experimental procedure was approved by the Committee of the Ethics on Animal Care and Experiments at Sichuan Agricultural University and was carried out in accordance with the approved guidelines. Based on our analysis, the genome of V. mimicus strain SCCF01 is 4.49 Mb in size and consists of 2 circular chromosomes of 3,213,040 and 1,272,975 bp with G+C content of 46.61% and 45.88%, respectively (Table 1). The following rules for bacterial subunit vaccine development, (1) it is often preferred to identify outer membrane(especially adhesins) or secreted proteins as vaccine targets. (2) more than one transmembrance helix is hard to be isolated from a recom-