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Genome characterization of novel lytic Myoviridae bacteriophage ϕVP-1 enhances its applicability against MDR-biofilm-forming Vibrio parahaemolyticus

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Abstract

A pathogen of significance in the aquaculture sector, the Gram-negative marine bacterium Vibrio parahaemolyticus causes gastroenteritis associated with consumption of improperly prepared seafood. This bacterium can be controlled using lytic bacteriophages as an alternative to antibiotics. ϕVP-1 is a lytic phage of V. parahaemolyticus that was isolated from an aquafarm water sample with the aim of assessing its potential as a bio-control agent and determining its physicochemical properties and genomic sequence. Morphological analysis by transmission electron microscopy and phylogenetic analysis based on the large terminase subunit gene showed that this phage belongs to the family Myoviridae. It could infect multiple-drug-resistant (MDR) V. parahaemolyticus and V. alginolyticus strains of mangrove and seafood origin. With a maximum adsorption time of 30 min, ϕVP-1 has a short latent period of 10 min with burst size of 44 particles/cell. Whole-genome sequencing was done using the Illumina platform, and annotation was done using GeneMarkS and Prodigal. The 150,764bp genome with an overall G+C content of 41.84% had 203 putative protein-encoding open reading frames, one tRNA gene, and 66 predicted promoters. A number of putative DNA replication and regulation, DNA packaging and structure, and host lysis genes were identified. Comparison of the ϕVP-1 genome sequence to those of known Vibrio phages indicated little discernible DNA sequence similarity, suggesting that ϕVP-1 is a novel Vibrio phage. Sequence analysis revealed the presence of 64 potential ORFs with a T4-like genomic organization. In silico analysis suggested an obligate lytic life cycle and showed the absence of lysogeny or virulence genes. The complete sequence of ϕVP-1 was annotated and deposited in the GenBank database (accession no. MH363700). The genetic features of this novel phage suggest that it might be applicable for phage therapy against pathogenic strains of V. parahaemolyticus.

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Acknowledgements

The authors acknowledge the Department of Biotechnology, Cochin University of Science and Technology, for providing all facilities for research. The first author acknowledges DST-PURSE for a Junior Research Fellowship.

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  1. Department of Biotechnology, Cochin University of Science and Technology, Kochi, Kerala, 682022, India

    Nandita Matamp & Sarita G. Bhat

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  1. Nandita Matamp
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Matamp, N., Bhat, S.G. Genome characterization of novel lytic Myoviridae bacteriophage ϕVP-1 enhances its applicability against MDR-biofilm-forming Vibrio parahaemolyticus. Arch Virol 165, 387–396 (2020). https://doi.org/10.1007/s00705-019-04493-6

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