Addressing the Challenges of Identifying Vibrio Species; Genomic and Phenotypic Analyses of Misidentified Vibrio vulnificus Strains Reveal Vibrio campbellii and a Potentially Novel V. rotiferianus-like Species in New Zealand Oysters

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Abstract
The genus Vibrio contains over 150 species of aquatic origin, some of which are important foodborne pathogens, while others cause diseases in finfish, shellfish and/or coral. Accurate identification of these bacteria is important, but highly challenging given their taxonomic diversity. Here we used a range of methods to identify strains from New Zealand oysters initially identified as Vibrio vulnificus. The API20E kit either misidentified, or failed to identify the strains depending on the database used; comparisons of the 16S rRNA gene sequences could not distinguish them from over 50 exemplars of other Vibrio spp. or Allocatenococcus thiocycli. Elastic light scatter analysis showed clear differences between each of the novel isolates and reference strains of Vibrio parahaemolyticus and V. vulnificus, but limits of the in-house database precluded identification. Our whole-genome sequencing (WGS) pipeline allowed genomes and plasmids to be effectively sequenced to completion, enabling in silico DNA-DNA hybridization analysis with 162 Vibrio spp., which identified the strains as either V. campbellii, or one that may represent a novel species closely related to V. rotiferianus. Genome analysis also revealed a variety of genes found in aquacultural and human pathogens, including V. cholerae. Furthermore, resistance to multiple antibiotic classes was indicated both genetically and phenotypically. The implications for New Zealand aquaculture and public health are discussed. WGS is an effective identification strategy for taxonomically complex bacteria such as Vibrio spp.
Funding Information
  • U.S. Department of Agriculture (58-8072-1-004-F)
  • China Scholarship Council
  • New Zealand Ministry of Business, Innovation and Employment (CAWX1801)

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