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Whole genome comparison of Vibrio harveyi strains from the Mediterranean Sea

In recent years, outbreaks of vibriosis are getting more common in the Mediterranean aquaculture, causing severe losses and threatening the long-term sustainability. In fact, in a three year period, from 2015 to 2017, the main reported disease in sea bass aquaculture in the Mediterranean was vibriosis. This disease is found in all parts of the Mediterranean Sea, and it is the most reported disease in the western, southern and eastern Mediterranean. Today Vibrio harveyi is recognized as one of the major causes of vibriosis, but there is a great heterogeneity in the virulence of different strains of V. harveyi. Unfortunately, little is known about the genomic differences in the strains of V. harveyi originating from different parts of the Mediterranean. We used eleven strains of V. harveyi isolated from fish originating from different parts of the Mediterranean Sea: four strains from Croatia, two from France, two from Italy, and one strain from Spain, Tunisia and Turkey. To obtain high-quality complete genome assemblies we performed high throughput sequencing using MiSeq (Illumina) and MinION (Oxford Nanopore Technologies) sequencers. For MiSeq sequencing genomic DNA was extracted from bacterial cultures using NucleoSpin Microbial DNA Mini kit, and the sequencing libraries were prepared using NexteraXT Library Prep Kit. For MinION sequencing DNA was extracted using Nanobind CBB Big DNA Kit and the libraries were prepared using Rapid Barcoding Kit. Whole genomes were assembled using Flye and Medaka tools with nanopore reads and corrected using the Racon polishing tool with Illumina reads. Larger deletions, inversions and translocations were detected using MAUVE multiple genome alignments. Virulence factors were identified in all of the genomes using VFDB pathogenomic platform, and the resistance genes were identified using the CARD RGI tool. The genomes of all eleven strains were successfully assembled, with BUSCO scores ranging from 97.58% to 100%. A comparison of the strains using the genomic determinants stated above will be presented in detail. Exploring the differences between strains of V. harveyi originating from different parts of the Mediterranean, and increasing the number of explored strains, we will obtain knowledge helpful in the determination of both local and regional management of vibriosis.

Vibrio harveyi, whole genome sequencing, Mediterranean Sea

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