First Report on Genome Analysis and Pathogenicity of Vibrio tubiashii FP17 from Farmed Ivory Shell (Babylonia areolata)

• Published in: Fishes 2022-12, Vol.7 (6), p.396
• Main Authors: Dai, Chen, Li, Xiaoxin, Luo, Dapeng, Liu, Qingming, Sun, Yun, Tu, Zhigang, Shen, Minghui
• Format: Article
• Language: English
• Subjects: Analysis; Antibiotics; Antimicrobial agents; Antimicrobial resistance; Aquaculture; Babylonia areolata; Chromosomes; Disease; DNA-directed RNA polymerase; Drug resistance; Electron microscopy; Epidemics; Flagella; Gene clusters; Genes; Genomes; Genomic analysis; Infections; Mollusks; Mortality; Mortality causes; Nucleotide sequence; Nucleotides; Open reading frames; Pathogenesis; Pathogenicity; Pathogens; Phylogenetics; Phylogeny; Plasmids; Polyculture (aquaculture); Proteins; rRNA 16S; Salinity; Secretion; Toxicity tests; Transmission electron microscopy; Vibrio tubiashii; Vibriosis; Virulence; Virulence factors; whole genome sequencing
• ISSN: 2410-3888; 2410-3888
• DOI: 10.3390/fishes7060396

Ivory shell (Babylonia areolata) is a commercially important aquaculture species mainly found on the southeast coast of China. However, it has been greatly affected by vibriosis in recent years. In this study, FP17 (a potential pathogen) was isolated from a dying ivory shell with “acute death syndrome” and confirmed as a pathogen via infectious experiment. Furthermore, phylogenetic analysis based on the average nucleotide identity (ANI) sequencing of the 16S rRNA gene and housekeeping genes (ftsz, gapA, gyrB, mreB, pyrH, rpoA, and topA) indicated that FP17 was identical to Vibrio tubiashii. Transmission electron microscopy showed that FP17 is curved and has a short rod shape, with a single flagellum. Besides, the calculated LD50 after the intramuscular injection of FP17 was 2.11 × 106 CFU/g at 14 d. The genome of the FP17 strain consists of two chromosomes and one plasmid with 5,261,336 bp and 45.08% GC content, including 4824 open reading frames (ORFs) and 150 non-coding RNAs (ncRNA). Genome mining revealed that 120 candidate gene clusters, including vibrioferrin and flagellum-related proteins, are responsible for virulence. Comparative genomic analysis showed that vibrioferrin genes, such as pvs and type Ⅵ secretion system protein genes (vas), are specific in V. tubiashii FP17 but not in the ATCC19109 strain. Furthermore, 92 antimicrobial resistance (AMR) genes, such as tufA, tet(35), crp, etc., were mapped within the genome as the potential candidate for virulence, consistent with antibiotic susceptibility assay. This is the first study to describe the complete genome sequence of V. tubiashii infecting ivory shell. The genetic characteristics, virulence factors, and antimicrobial resistance of the V. tubiashii strain FP17 were also explored.