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Complete genome sequence of pathogenic Vibrio alginolyticus EBVib0155 isolated from seawater, South Korea
Korean J. Microbiol. 2024;60(1):35-37
Published online March 31, 2024
© 2024 The Microbiological Society of Korea.

Hyunwoo Zin* , Byeri Kim, Miseon Jang, Myeonghye Jeong, Sein Lee, Intae Ham, Soonbum Shin, Ka Jeong Lee, Kwang Soo Ha, Hongsik Yu, and Jong soo Mok

Food Safety and Processing Research Division, Gijang, Busan 46083, Republic of Korea
Correspondence to: *E-mail: zinhyunwoo@korea.kr;
Tel.: +82-51-720-2633; Fax: +82-51-720-2619
Received November 22, 2023; Revised December 19, 2023; Accepted December 20, 2023.
Abstract
Vibrios are a group of Gram-negative bacteria known for causing food poisoning outbreaks globally. This study unveils the complete genome sequence of Vibrio alginolyticus strain EBVib0155, isolated from seawater in the southeast sea of South Korea. The complete genome of Vibrio alginolyticus strain EBVib0155 comprises two chromosomal DNA. The first chromosome spans 3,324,308 bp, while the second chromosome spans 1,889,638 bp, with 45.4% and 45.3% GC content, respectively. Gene prediction analysis revealed 2,985 CDSs, 118 tRNAs and 34 rRNAs in the first chromosome, along with 1,690 CDSs, 14 tRNAs and 3 rRNAs in the second chromosome.
Keywords : Vibrio alginolyticus, complete genome, food poisoning
Body

Vibrios are a group of Gram-negative bacteria commonly associated with food poisoning, typically found in marine, estuarine, and coastal environments (Oliver et al., 2013; Letchumanan et al., 2014). Strains of Vibrio spp. are often linked to waterborne gastroenteritis, primarily associated with the consumption of raw or undercooked seafood (McLaughlin et al., 2005). These bacteria have a significant history of public health concern, contributing to major food poisoning outbreaks on a global scale (Hasan et al., 2015; Onohuean et al., 2022), notably affecting shellfish harvesting environments or shellfish such as oysters and clams (CDC, 1999). Vibrio species within the Vibrionaceae family (Letchumanan et al., 2014) is frequently present in shellfish and marine environment. Vibrio parahaemolyticus is known to possess two well-known hemolytic virulence factors, thermostable direct hemolysin (tdh) and TDH-related hemolysin (trh). These pore-forming proteins contribute to the bacterium’s invasiveness in humans (Raghunath, 2015). In this study, we investigated the isolation of a unique Vibrio alginolyticus strain possessing virulence factors commonly associated with pathogenic Vibrio, particularly those found in Vibrio parahaemolyticus.

The Vibrio alginolyticus strain EBVib0155 was isolated from seawater adjacent to Mireuk-do in southeast sea (Gyeongsangnam-do province) of South Korea. Genomic DNA extraction for EBVib0155 was conducted using a Bacterial Genomic DNA Extraction Kit Ver. 3.0 (Takara, MiniBEST), and genome sequencing was performed using the PacBio Sequel sequencing platform. The high-quality genomic DNA was sheared using a G-tube device (Covaris), and the sheared DNA was used to prepare a PacBio library. The library was then sequenced using a single-molecule real-time (SMRT) sequencing system, resulting in a total of 583,475 sequence reads with an N50 value of 10,129, and a mean length of 8,599 that were assembled into 2 contigs. The raw sequence reads were de novo assembled using HGAP, resulting in a final assembly with a coverage (depth) of 962X. Additionally, the resulting asymmetric structure was validated using Circlator (version 1.5.5) to ascertain its circular or linear form. Genome annotation was performed using the NCBI prokaryotic genome annotation pipeline (Tatusova et al., 2016).

The genome of Vibrio alginolyticus strain EBVib0155 comprises two chromosomal DNA. The first chromosome spans 3,324,308 bp, while the second chromosome spans 1,889,638 bp, with 45.4% and 45.3% GC content, respectively. Gene prediction analysis revealed 2,985 CDSs, 118 tRNAs and 34 rRNAs in the first chromosome, along with 1,690 CDSs, 14 tRNAs and 3 rRNAs in the second chromosome (Table 1).

Genome features of Vibrio alginolyticus EBVib0155

Feature Chromosome 1 (EBVib0155C1) Chromosome 2 (EBVib0155C2)
Size (bp) 3,324,308 1,889,638
G + C contents (%) 45.4% 45.3%
Total number of
CDSs 2,985 1,690
rRNA genes (5S, 16S, 23S) 34 (12, 11, 11) 3 (1, 1, 1)
tRNA genes 118 14
Pseudo genes 570 332
GenBank Accession No. CP128370 CP128371


The study of bacteria with multiple virulence factors is important. As in the case of the food poisoning bacteria that emerged in Germany in 2011 and subsequently spread throughout Europe and North America (Karch et al., 2012), it was identified as a hybrid strain with one or more pathogenic factors. The Vibrio alginolyticus strain EBVib0155 isolated in this study, the in silico Virulence Factor Database (Liu et al., 2019) identified virulence and related genes (Fig. 1), including thermostable direct hemolysin (tdh, locus tag: QSJ11_19040) and TDH-related hemolysin (trh, locus tag: QSJ11_20010). This finding is unusual, as in the case of Vibrio alginolyticus, it is rare for it to possess virulence factors such as tdh and trh. Furthermore, these virulence factors are primarily associated with genes found in Vibrio parahaemolyticus. Understanding the genetic makeup and virulence factors of food poisoning bacteria is crucial for public health and food safety. This information can contribute to the development of strategies aimed at mitigating the risks associated with its consumption and preventing outbreaks of foodborne illnesses.

Fig. 1. Genome map of pathogenic Vibrio alginolyticus EBVib0155. The graphical circular maps are shown of the alignment of genes and other genomic data. The tracks on the viewer are displayed as concentric rings, from outermost to innermost: Forward CDS, Reverse CDS, GC Skew, GC contents, AMR genes, VF genes, transporters and drug target. Genes with specialized functions labeled with different colors as virulence-related genes in red, and other functional genes such as antimicrobials resistance, transporters, drug target as yellow, blue, and black.

Nucleotide sequence accession number(s)

Nucleotide sequence accession numbers. The complete genome sequence of Vibrio alginolyticus EBVib0155 has been deposited at the NCBI GenBank database under the accession numbers CP128370 (chromosome 1, EBVib0155C1), CP128371 (chromosome 2, EBVib0155C2) and the strain has been deposited in the Korean Culture Collection of Aquatic Microorganisms (KoCAM) under the strain number EBVib0155.

적 요

비브리오는 전 세계적으로 식중독 발병을 일으킬 수 있는 그람 음성 세균이다. 본 연구에서 분리된 균주는 대한민국 남동해 해역 해수에서 분리된 Vibrio alginolyticus EBVib0155 균주로 전장 유전체 서열 분석을 실시하였다. Vibrio alginolyticus EBVib0155의 전장 유전체 분석결과 두 개의 염색체가 확인되었으며, 첫 번째 염색체는 3,324,308 bp, 두 번째 염색체는 1,889,638 bp로 각 45.4% 및 45.3%의 GC 함유량이 확인되었다. 또한, 유전자 예측 분석에 따르면 첫 번째 염색체에는 2,985개의 CDSs, 118개의 tRNA 및 34개의 rRNA, 두 번째 염색체에는 1,690개의 CDSs, 14개의 tRNA 및 3개의 rRNA로 확인되었다.

Acknowledgments

This research was financially supported by the National Institute of Fisheries Science, Republic of Korea (R2023054).

Conflict of Interest

The authors have no conflict of interest to report.

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