RESEARCH ARTICLE

Analysis of whole genome sequencing and virulence factors of Vibrio vulnificus 1908-10 isolated from sea water at Gadeok island coast

Hee-kyung Oh1https://orcid.org/0009-0004-6172-9863, Nameun Kim2https://orcid.org/0000-0002-0366-5871, Do-Hyung Kim2https://orcid.org/0000-0001-7315-1297, Hye-Young Shin3https://orcid.org/0000-0003-1669-6586, Eun-Woo Lee4https://orcid.org/0000-0003-4091-6606, Sung-Hwan Eom5https://orcid.org/0000-0002-5812-8846, Young-Mog Kim6,*https://orcid.org/0000-0002-2465-8013
Author Information & Copyright
1Marine Products Sanitary Control Center, Dong-Eui University, Busan 47340, Korea
2Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea
3Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangneung 25457, Korea
4Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan 47340, Korea
5Department of Food Science and Technology, Dong-Eui University, Busan 47340, Korea
6Department of Food Science and Technology, Pukyong National University, Busan 48513, Korea
*Corresponding author: Young-Mog Kim, Department of Food Science and Technology, Pukyong National University, Busan 48513, Korea, Tel: +82-51-629-5832, Fax: +82-51-629-5824, E-mail:ymkim@pknu.ac.kr

Copyright © 2023 The Korean Society of Fisheries and Aquatic Science. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: May 09, 2023; Revised: Jul 03, 2023; Accepted: Jul 08, 2023

Published Online: Sep 30, 2023

Abstract

Vibrio vulnificus is an aquatic bacterium causing septicemia and wound infection in humans. To understand this pathogen at the genomic level, it was performed whole genome sequencing of a cefoxitin-resistant strain, V. vulnificus 1908-10 possessing virulence-related genes (vvhA, viuB, and vcgC) isolated from Gadeok island coastal seawater in South Korea. The genome of V. vulnificus 1908-10 consisted of two circular contigs and no plasmid. The total genome size was estimated to be 5,018,425 bp with a guanine-cytosine (GC) content of 46.9%. We found 119 tRNA and 34 rRNA genes respectively in the genome, along with 4,352 predicted protein sequences. Virulence factor (VF) analysis further revealed that V. vulnificus 1908-10 possess various virulence genes in classes of adherence, antiphagocytosis, chemotaxis and motility, iron uptake, quorum sensing, secretion system, and toxin. In the comparison of the presence/absence of virulence genes, V. vulnificus 1908-10 had fur, hlyU, luxS, ompU, pilA, pilF, rtxA, rtxC, and vvhA. Of the 30 V. vulnificus comparative strains, 80% of the C-genotype strains have all of these genes, whereas 40% of the E-genotype strains have all of them. In particular, pilA were identified in 80% of the C-type strains and 40% of the E-type strains, showing more difference than other genes. Therefore, V. vulnificus 1908-10 had similar VF characteristics to those of type C strains. Multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin of V. vulnificus 1908-10 contained 8 A-type repeats (GXXGXXXXXG), 25 B.1-type repeats (TXVGXGXX), 18 B2-type repeats (GGXGXDXXX), and 7 C-type repeats (GGXGXDXXX). The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) showed that the RtxA protein of V. vulnificus 1908-10 had the effector domain in the order of cross-liking domain (ACD)-C58_PaToxP-like domain- α/β hydrolase-C58_PaToxP-like domain.

Keywords: Vibrio vulnificus; whole genome sequencing; virulence factor; multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin

Introduction

Vibrio vulnificus is an aquatic bacterium infected with ingestion of raw or undercooked seafood or with exposure of wounds to seawater causing gastroenteritis, wound infection, and sepsis. In the case of primary sepsis, the fatality rate reaches more than 50% (Hlady & Klontz, 1996; Oliver, 2005; Shapiro et al., 1998). In South Korea, where seafood intake is high, V. vulnificus has been steadily detected nationwide, and 37 to 88 cases of Vibrio sepsis have been reported every year from 2000 to 2020, and the mortality rate is 45.7% from 2011 to 2020 (Cho & Park, 2019; KDCA, 2021; Kim et al., 1987; 1990; Park et al., 2019). V. vulnificus has several virulence factors (VF) such as capsular polysaccharide (CPS), iron uptake, hemolysin (vvhA), protease (vvpE), repeats-in-toxin (RTX) toxin, lipopolysaccharide, pili, and flagella, and various factors regulating them have been reported for the pathogenicity of V. vulnificus, and studies such as identification of the toxic activation mechanisms have been conducted, too (Jones & Oliver, 2009; Lee et al., 2019).

Along with the development of next-generation sequencing technology, genome analysis of many pathogenic bacteria important in public health has been performed, and in the case of V. vulnificus, starting with the first genome report in 2003, whole genome analysis has been conducted to identify genomic characteristics and various attempts are being made such as comparison between clinical and environmental genotypes (Chen et al., 2003; Morrison et al., 2012; Pan et al., 2017; Pang et al., 2020; Roig et al., 2018). However, compared to other pathogenic bacteria such as Salmonella enterica and Staphylococcus aureus, the genome analysis of V. vulnificus is insignificant, and even compared to the same genus Vibrio, it is less than that of Vibrio parahaemolyticus and Vibrio cholerae (NCBI, 2023).

The eastern coast of Gadeok island is provided good conditions for the habitat of V. vulnificus due to the inflow of the Nakdong river. Additionally, the final treated water from three sewage treatment plants is flowing in this area, and it is possible to influx pollutants from the land. Our previous studies identified the detection tendency of V. vulnificus in the seawater of the eastern coast of Gadeok island, the genetic characteristics related to pathogenicity, and the antibiotic resistance characteristics of the isolates (Oh et al., 2020, 2021). In this study, whole genome sequencing analysis was performed on the pathogenic V. vulnificus isolated from the coast of Gadeok island, and the characteristics of VFs were looked for.

Materials and Methods

Bacterial strain and DNA extraction

V. vulnificus 1908-10 used for whole genome sequencing analysis was isolated in August 2019 from the seawater of the eastern coast of Gadeok island in a previous study (Oh et al., 2020, 2021). This strain possessed virulence-related genes (vvhA, viuB, and vcgC), β-hemolysis activity, and cefoxitin resistance (minimal inhibitory concentration 32 μg/mL). The strain was cultured at 35°C with Luria-Berani broth (NEOGEN, Lancing, MI, USA) supplemented with 1% NaCl for 12 h, and the genomic DNA was extracted using Genomic DNA extraction kit (Bioneer, Daejeon, Korea) according to the manufacturer’s procedure.

Whole genome sequencing and annotation

Two different genomic DNA libraries were constructed according to the manufacturer’s instructions for the Illumina and the PacBio platform. Sequencing was performed using PacBio Sequel I System (Pacific Biosciences, Menlo Park, CA, USA) and Illumina HiSeqX ten sequencer (Illumina, San Diego, CA, USA). CANU v1.7 (Koren et al., 2017) and Pilon v1.21 (Walker et al., 2014) were used for de novo assembly. The completeness of the genomic data was assessed by B U SCO v5.1.3 (Manni et al., 2021). The genome sequences of V. vulnificus 1980-10 were deposited in the National Center for Biotechnology Information (NCBI) GenBank server under the accession numbers CP118438 and CP118439 for chromosome I and II. Gene annotation was conducted using prokka v1.13 (Seemann, 2014), eggnog 4.5 (Huerta-Cepas et al., 2016) and PATRIC v.3.6.12 (Wattam et al., 2017). The functional classification for coding sequences was performed through Position-Specific Iterative Basic Local Alignment Search Tool (PSI-BLAST; https://blast.ncbi.nlm.nih.gov/Blast.cgi) based on the Clusters of Orthologous Genes (COGs) database (2014 update version; http://www.ncbi.nlm.nih.gov/COG/) and was visualized with a circular map using CIRCOS v.0.69-63 (http://circos.ca).

Comparative genome analysis

The identity of V. vulnificus 1908-10 was confirmed by comparative phylogenetic analysis using MEGA11 v.11.08 (Tamura et al., 2021) against 16S rRNA sequences of the genus Vibrio. A verage nucleotide identity (ANI) matrix was constructed via EDGAR 3.0 (Dieckmann et al., 2021). The NCBI dataset was used for comparative genomic analysis of V. vulnificus in this study (Table 1).

Table 1. Attributes of Vibrio vulnificus used for comparative genomic analysis in this study
Strain name Genotype Isolation source Country Collected year Size (Mb) Accession No.
V. vulnificus
 07-2444 C Blood USA 2007 5.23 GCA_009764115.1
 1676-80 C Water USA Unknown 5.04 GCA_012275045.1
 2497-87 E Blood USA Unknown 5.03 GCA_014211935.1
 93U204 C Oreochromis Taiwan 2004 5.13 GCA_000746665.1
 ATCC 27562 E Human blood USA 1979 5.01 GCA_002224265.1
 CECT4606 E Healthy eel Spain 1990 5.19 GCA_002891755.1
 CECT4999 E Diseased eel Spain 1990 5.16 GCA_002215135.1
 CECT7030 E Eel Denmark 2004 5.11 GCA_002903505.1
 CECT898 E Eel Japan 1979 5.20 GCA_002903765.1
 CG100 C Oyster Taiwan 1993 5.21 GCA_002903465.1
 CladeA-yb158 C Tilapia Israel 2005 5.29 GCA_001013325.1
 CMCP6 C Human South Korea 2003 5.13 GCA_004355205.1
 Env1 E Oyster USA Unknown 4.95 GCA_003047125.1
 FDAARGOS_119 E Human USA Unknown 4.98 GCA_001558515.2
 FDAARGOS_663 E Human USA Unknown 4.97 GCA_008693685.1
 FORC_017 C Human blood South Korea 2014 5.23 GCA_001675245.1
 FORC_036 C Mactra veneriformis South Korea Unknown 6.07 GCA_002117205.1
 FORC_037 C Mya arenaria oonogai Makiyama South Korea Unknown 5.12 GCA_002204915.1
 FORC_053 E Mactra veneriformis South Korea 2013 6.02 GCA_003522555.1
 FORC_054 E Konosirus punctatus South Korea 2014 5.12 GCA_002863725.1
 FORC_077 C Human South Korea 2017 5.02 GCA_004319645.1
 JY1305 E Oyster USA Unknown 4.95 GCA_000269725.1
 JY1701 E Oyster USA Unknown 4.94 GCA_000269765.1
 LSU1015 C Human USA Unknown 5.59 GCA_002906245.1
 MO6-24/O C Human South Korea Unknown 5.01 GCA_000186585.1
 Vv180806 C Human blood China 2018 5.36 GCA_014107515.1
 VV2014DJH E Human blood China 2014 5.07 GCA_002850455.1
 VVyb1(BT3) E Tilapia Israel 2004 5.75 GCA_000342305.2
 YJ016 C Human blood Taiwan < 2003 5.26 GCA_000009745.1
Vibrio parahaemolyticus RIMD 2210633 Human Japan 1996 5.17 GCA_000196095.1
V. parahaemolyticus DLM1799 Seawater China 2019 5.11 GCA_023205915.1
Vibrio cholerae RFB16 Fresh water USA 2017 4.14 GCA_008369605.1
V. cholerae 1154-74 Diarrhea India 1974 3.93 GCA_000969235.1
Clostridium perfringens ATCC13124 Type strain Unknown Unknown 3.26 GCA_000013285.1
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Identification of virulence factors and multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin

The VFs of the V. vulnificus 1908-10 genome were analyzed using the virulence factor database (VFDB) 2019 (Liu et al., 2019) and their locations were edited on a visualized circular map using Adobe Photoshop 2023. Virulence gene presence/absence comparison was performed by obtaining comparison strains information from the NCBI dataset and reannotating using prokka. We used PROSITE (Sigrist et al., 2012) to find multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin repeat regions and used MEGA 11 to identify the number and location of repeat sequences described by Roig et al. (2011). NCBI BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) was used to perform and compare searches for the effector domains.

Antimicrobial resistance genes

The search for antibiotic resistance genes in V. vulnificus 1908-10 was performed using ResFinder (Bortolaia et al., 2020) and Comprehensive Antibiotic Resistance Database (CARD) (Alcock et al., 2020).

Results and Discussion

Genome properties and annotation

As a result of whole genome analysis, V. vulnificus 1908-10 was composed of two circular contigs, and no plasmid was identified. The total length of the genome was 5,018,425 bp, and its GC content was 46.9%. Contigs 1 and 2 were 3,273,700 bp and 1,744,725 bp long, respectively, with 46.7% and 47.3% corresponding guanine-cytosine (GC) contents. Total coding sequences (CDS) were 4,352, with 2,890 in contig 1 and 1,462 in contig 2. 119 tRNAs and 34 rRNAs were identified and were mainly distributed in contig 1 (Table 2).

Table 2. Summary of whole-genome sequencing for Vibrio vulnificus 1908-10
Property V. vulnificus 1908-10
Methods reads
 PacBio Sequel I System
  Total filtered subreads 169,959
  N50 12,142
 Illumina HiSeqX ten
  Total filtered reads 8,211,314
  Q30 (%) 98.16
Results of assembly Contig 1 Contig 2 Total
 Contigs 1 1 2
 Total contig bases 3,273,700 1,744,725 5,018,425
 N50 3,273,700
 GC (%) 46.7 47.3 46.9
 Depth 326.8 272.0 307.8
Genome annotation
 CDS 2,890 1,462 4,352
 tRNA 106 13 119
 rRNA 31 4 34

GC, guanine-cytosine; CDS, coding sequence.

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As a result of analysis based on the COGs, the genome of V. vulnificus 1908-10 had the most genes related to metabolism at 31.6%, genes related to cell processing and signals at 29.3% and genes related to information storage and process were 16.2%. Mobilome-related genes such as prophages and transposons were 1.8% (Fig. 1). In detail, genes involved in signal transduction mechanisms were the most common at 8.3%, followed by genes involved in transcription at 7.1%, genes involved in amino acid transport and metabolism at 6.8%. Genes involved in cell wall/membrane/envelope biogenesis were 5.7%. The COGs of V. vulnificus Vv180806 and V. vulnificus VV2014DJH have been reported and generally show similar trends. However, in the cytoskeleton category, V. vulnificus Vv180806 and V. vulnificus VV2014DJH had no corresponding genes, while two genes were identified in V. vulnificus 1908-10 showing differences (Pan et al., 2017; Pang et al., 2020).

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Fig. 1. Functional classification of the protein coding sequence in Vibrio vulnificus 1908-10 based on COG categories. COG, clusters of orthologous gene.
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Phylogenetic tree and average nucleotide identity (ANI)

In a phylogenetic analysis comparing 16s rRNA using MEGA 11 software, this strain was identified as V. vulnificus distinct from other Vibrio spp. and outgroup (Fig. 2 A). When comparing the similarity of genomes using EDGAR based on the NCBI dataset, V. vulnificus 1908-10 was the most similar to V. vulnificus FORC_077, with about 99.41% similarity, followed by V. vulnificus CMCP6 and V. vulnificus FORC_053 was 99.02%. V. vulnificus FORC_017 followed with 98.92%. Strain FORC_077, CMCP6, and FORC_017 were of type C, often found in clinically isolated strains when classified based on genotype. V. vulnificus FORC_053 was of type E. Twelve (80%) of the top 15 isolates with an ANI greater than 98% were type C, so V. vulnificus 1908-10 was similar to type C overall (Fig. 2B). 95 % ANI corresponded to the recommended cut-off point for species delineation (Goris et al., 2007).

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Fig. 2. Phylogenetic tree based on 16S rRNA sequence (A) and median ANI matrix tree (B) of Vibrio vulnificus 1908-10. ANI, average nucleotide identity.
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Identification of virulence factors

As a result of analyzing through VFDB, V. vulnificus 1908-10 had genes of VFs such as mannose-sensitive hemagglutinin type IV pilus, CPS, flagella, metalloproteinase, vibriobactin related to iron absorption, heme receptor, and periplasmic binding ATP binding cassette (ABC) protein transport system. It possessed the luxS gene of autoinducer-2 in the quorum sensing class, and among the secretion systems, the EPS type II secretion system was identified. Toxin factors like vvhA, tlh, and RTX gene clusters (rtxABCD) were identified (Table 3). Genes related to attachment, motility, and secretion systems were located in contig 1 of the genome, while genes for metalloproteinases, iron uptake vibriobactin, transport systems, and toxins such as hemolysin and RTX were identified in contig 2. CPS genes were identified in both contig 1 and contig 2 (Fig. 3). CPS has been reported to be biochemically and genetically diverse among strains (Pettis & Mukerji, 2020), and V. vulnificus 1908-10 was found to have cpsABCDFHIJ, hp1, wbfU, wbfV/wcvB, wbfY, wza, wzb, and wzc (Table 3).

Table 3. Virulence factors of Vibrio vulnificus 1908-10 identified using the virulence factor database
Virulence class Virulence factors and genes
Presence Absence
Adherence MSHA type IV pilus
-mshA, mshB, mshC, mshD, mshE, mshF, mshG, mshH, mshI, mshJ, mshK, mshL, mshM, mshN
Type IV pilus
-pilA, pilB, pilC, pilD
Accessory colonization factor
-acfA, acfB, acfC, acfD
Toxin-coregulated pilus (typeIVB pilus)
-tcpD, tcpE, tcpF, tcpH, tcpI, tcpJ, tcpN/toxT, tcpP, tcpQ, tcpR, tcpS, tcpT
Antiphagocytosis Capsular polysaccharide
-cpsA, cpsB, cpsC, cpsD, cpsF, cpsH, cpsI, cpsJ, hp1, wbfU, wbfV/wcvB, wbfY, wza, wzb, wzc
Capsular polysaccharide
-cpsE, cpsG, rmlA, rmlB, rmlC, rml D, wbfB, wbfC, wbfT, wbjD/wecB, wbuB, wcaJ, wecA, wecC
Chemotaxis and motility Flagella
-cheA, cheB, cheR, cheV, cheW, cheY, cheZ, filM, flaA, flaB, flaC, flaD, flaE, flaG, flaI, flgA, flgB, flgC, flgD, flgE, flgF, flgG, flgH, flgI, flgJ, flgK, flgL, flgM, flgN, flhA, flhB, flhF, flhG, fliA, fliD, fliE, fliF, fliG, fliH, fliI, fliJ, fliK, fliL fliM, fliN, fliO, fliP, fliQ, fliR, fliS, flrA, flrB, flrC, motA, motB, motX, motY
Flagella
-flaC
Enzyme Metalloproteinase
-hap/vvp
Neuraminidase
-nanH
Iron uptake Heme receptors
-hutA, hutR
Periplasmic binding protein dependent ABC transport systems
-vctC, vctD, vctG, vctP
Vibriobactin
-vibA, vibB, vibC, vibD, vibE, vibF, vibH, viuA, viuB
Enterobactin receptors
-irgA, vctA
Heme receptors
-hasR
Periplasmic binding protein dependent ABC transport systems
-viuC, viuD, viuG, viuP
Quorum sensing Autoinducer-2
-luxS
Secretion system EPS type II secretion system
-epsC, epsE, epsF, epsG, epsH, epsI, epsJ, epsK, epsL, epsM, epsN, gspD
VAS effector proteins
-hcp-1, hcp-2, vgrG-1, vgrG-2, vgrG-3
VAS type VI secretion system
-vasA, vasB, vasC, vasD, vasE, vasF, vasG, vasH, vasI, vasJ, vasK
Toxin Hemolysin/cytolysin
-vhA
RTX toxin
-trxA, rtxB, rtxC, rtxD
Thermolabile hemolysin
-tlh

MSHA, mannose-sensitive hemagglutinin; ABC, ATP binding cassette; EPS, extracellular protein secretion; VAS, virulence associated secretion; RTX, repeats-in-toxin.

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fas-26-9-558-g3
Fig. 3. Circular genome maps of Vibrio vulnificus 1908-10 based on COGs and VFDB analysis. A: Contig 1. B: Contig 2. Marked characteristics are shown from outside to the center; CDS on forward strand, CDS on the reverse strand, tRNA (green), rRNA (red), GC content and GC skew. All annotated ORFs were colored differently according to the COG assignments. COG, clusters of orthologous gene; VFDB, virulence factor database; CDS, coding sequence; GC, guanine-cytosine.
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Compared to the 29 V. vulnificus strains in the NCBI dataset, V. vulnificus 1908-10 had fur, hlyU, luxS, ompU, pilA, pilF, rtxA, rtxC, and vvhA genes. All 30 strains including 1908-10, had hlyU, ompU, pilF, and vvhA genes in common. On the other hand, fur was identified in 96.7%, rtxA in 90%, luxS in 83.3%, rtxC in 76.7% and pilA in 60% of the strains. Particularly, pilA, which is part of the type IV pili operon, was found in 80% of type C strains but in 40% of type E strains, showing differences between genotypes (Table 3 and Fig. 4). hlyU regulates the expression of rtxA1 at the transcriptional level, affecting its cytotoxicity and virulence (Liu et al., 2007). ompU is a factor involved in bacterial adhesion to host cells (Goo et al., 2006). pilF is a protein gene required for the assembly of type IV pili, whose functions include surface motility of the strain, colony, and biofilm formation, and host cell adhesion (Alm & Mattick, 1997; Hobbs & Mattick, 1993). vvhA is a hemolysin/cytolysin gene of V. vulnificus.Fur regulates the production of hemolysin, rtxA encodes the RTX toxin and rtxC encodes the toxin activator (Lee et al., 2013; Lin et al., 1999). luxS is an autoinducer-2 synthase gene in the quorum sensing system and has been reported to affect the transcription of vvhA and vvpE (Kim et al., 2003). Overall, V. vulnificus 1908-10 had more similar virulence characteristics to type C strains, as 80% of type C strains had all nine genes compared, while 40% of type E strains did.

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Fig. 4. Comparison of virulence genes of Vibrio vulnificus 1908-10 and other V. vulnificus strains.
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Multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin

MARTX toxins are large single polypeptide toxins produced by various gram-negative bacteria. They deliver numerous effector proteins from the bacteria to the host cell to alter the target cell physiology. In contrast to the conservation of the MARTX toxin domain structure among most of the V. cholerae isolates, the V. vulnificus MARTX toxins are strikingly diverse (Kim, 2018; Satchell, 2015). Ten different effector domains have been recognized among the various MARTX toxins of Vibrio spp., although any one toxin carries only two to five effectors (Satchell, 2015). MARTX toxin of V. vulnificus 1908-10 contained 8 A-type repeats (GXXGXXXXXG), 25 B.1-type repeats (TXVGXGXX), 18 B2-type repeats (GGXGXDXXX), and 7 C-type repeats (GGXGXDXXX). NCBI BLAST showed that the RtxA protein of V. vulnificus 1908-10 had the effector domain in the order of actin cross-liking domain (ACD)-C58_PaToxP-like domain-α/β hydrolase-C58_PaToxP-like domain (Fig. 5), with the same domain sequence as V. vulnificus FORC_017, V. vulnificus FORC_053, and V. vulnificus CECT4999 (NCBI, 2023). Their amino acid sequence of the effector domain was 100% identical to V. vulnificus FORC_017, but there were differences in some amino acids when compared to V. vulnificus FORC_053 and V. vulnificus CECT4999. ACD disrupts the cell cytoskeleton and inhibits the engulfing activity of phagocytic immune cells of the host. α/β hydrolases reduce the intracellular phosphatidylinositol 3-phosphate levels and blocked autophagic/endosomal pathways. The C58_PaToxP-like domain, also known as makes caterpillars floppy-like domain (MCF), is associated with apoptotic cell death (Kim, 2018).

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Fig. 5. rtx gene cluster (A) and domain organization of the MARTX toxin (B) of Vibrio vulnificus 1908-10. MARTX, multifunctional-autoprocessing repeats-in-toxin.
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V. vulnificus FORC_077, which had a high ANI value for its genome, had the effector domain sequence of membrane localization domain (MLD)-α/β hydrolase-C58_PaToxP-like domain. V. vulnificus CMCP6 and YJ016 had domains of MLD-α/β hydrolase-C58_PaToxP-like domain–toxin_MLD (toxin effector region membrane localization domain)-RtxA-like domain (C2-2 like domain of various multidomain toxins) (NCBI, 2023). Biochemical mechanisms and direct target molecules for specific effector domains of MARTX toxins have been characterized, but some still require further study (Kim, 2018). Meanwhile, the diversity of effector domains in the MARTX toxin was independent of genotype (data not shown).

Antimicrobial resistance genes

Regarding antibiotic resistance in V. vulnificus 1908-10, no acquired resistance genes were identified in the analysis using ResFinder. On the other hand, CARD analysis identified the antibiotic resistance genes crp, adeF, varG, parE, and ftsI in this strain. Of these, ftsI was detected from a protein variant model associated with antibiotic target alteration in cephalosporins, but whether it was a factor of cefoxitin resistance in this strain requires further study (data not shown).

Genome analysis of V. vulnificus 1908-10 isolated from the eastern coast of Gadeok-do r evealed that this strain was similar to C-genotype V. vulnificus in terms of ANI and VFs. MARTX toxin sequence was identified also. V. vulnificus is continuously threatening food hygiene and public health. Among strains that genomes have been reported in South Korea, there has been no report of isolates from riverine seawater. The genomic information of this strain can be used as basic data for the genome of the strain according to the isolation environment as well as understanding the genomic characteristics and virulence of V. vulnificus.

Competing interests

No potential conflict of interest relevant to this article was reported.

Funding sources

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2021R1A6A1A03039211).

Acknowledgements

Not applicable.

Availability of data and materials

Upon reasonable request, the datasets of this study can be available from the corresponding author.

Ethics approval and consent to participate

This study conformed to the guidance of animal ethical treatment for the care and use of experimental animals.

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