Progress in Microbes and Molecular Biology Genome Report 1 Genome sequence of Vibrio sp. SALL 6 isolated from shellfish Vengadesh Letchumanan1*, Hooi-Leng Ser1,2, Tan Wen-Si3,4, Kok-Gan Chan4,5, Nurul-Syakima Ab Mu- talib6 1Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia 2Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, P. R. China 3Illumina Singapore Pte Ltd, Woodlands Industrial Park E1, Singapore 4Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 5International Genome Centre, Jiangsu University, Zhenjiang 212013, PR China 6UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, University Kebangsaan Malaysia, Kuala Lum- pur, Malaysia Abstract : Members of the Vibrionaceae family are well known as foodborne pathogen that cause hazard to human in many forms of clinical infection and also affecting aquaculture via infection to livestock. This pathogen has caused seafood associ- ated gastroenteritis cases in many countries including United States, Asian, and South East Asian countries. Antibiotics are usually used as prophylactic and therapeutic to manage the rising Vibrio infections, however, this in turn led to emergence of antibiotic resistant strains in the environments. Vibrio sp. SALL 6 isolated from shellfish was selected for genome sequencing to further explore its antimicrobial traits. Here, a high-quality genome sequence of Vibrio sp. SALL 6 is reported, while its genome reveals a potential for future antibiotic resistance managements. Keywords: Vibrionaceae; foodborne; gastroenteritis; antibiotics; genome Received: 26th October 2019 Accepted: 26th November 2019 Published Online: 06th December 2019 Citation: Letchumanan V, Ser H-L, Tan W-S, et al. Genome sequence of Vibrio sp. SALL 6 isolated from shellfish. Prog Microbes Mol Biol, 2019; 2(1): a0000044 Introduction Vibrio species are natural inhabitant of aquatic environ- ments and are the main cause of seafood-borne gastroen- teritis[1,2]. This Gram-negative halophilic bacteria belong to the Vibrionaceae family[3–5] and many of them are linked with aquatic animals such as crustaceans, molluscs and fish[6]. Of the 12 identified pathogenic Vibrio sp., the three commonly reported are Vibrio cholerae and Vibrio para- haemolyticus — associated with seafood contamination, and Vibrio vulnificus — related via wound infections[7,8]. The increase in seafood consumption worldwide lead to the global rise of seafood production from aquaculture. This causes the marine animals to be prone to bacterial infections[9]. The occurrence of Vibrio sp. in our environ- ments does raise a public concern on food safety due to the rising number of reported foodborne cases worldwide[10]. This situation has worsen by the emergence of antibiotic resistant bacteria which cause a delay in treatment, pro- long hospitalization and even mortality. Antibiotics are used in the aquaculture sector to treat bacterial infec- tion, however, the misuse of them has resulted in the rising number of resistant foodborne pathogens such as Vibrio sp.[11–18], Listeria sp.[19,20], and Salmonella sp.[21–24]. Antibiotic resistance among foodborne pathogens is a major health issue and a great challenge to worldwide drug discovery programmes[25]. The clinical and envi- ronmental Vibrio sp. strains are reported to exhibit an- tibiotic resistance traits[26]. Hence, it is vital to continu- ously monitor and manage the occurrence of Vibrio in seafood and environments. Vibrio sp. SALL 6 strain was isolated from shellfish originated from a wetmarket in Selangor, Malaysia. It formed green colony on thiosulphate citrate bile salt su- crose (TCBS) agar. The strain exhibited multidrug resis- tance profile towards 3/14 antibiotics tested. Based on the antibiotic susceptibility phenotype, Vibrio sp. SALL Copyright 2019 by Letchumanan V et al. and HH Publisher. This work under licensed under the Creative Commons Attribution-Non- Commercial 4.0 International Lisence (CC-BY-NC 4.0) *Correspondence: Vengadesh Letchumanan, Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; lvengadesh@yahoo.com. 2 6 strain was resistant to ampicillin, 3rd generation cepha- losporin (cefotaxime) and aminoglycoside (amikacin). This is a distressing condition as the antibiotic resistant profile shown by this strain is among the recommended antimicrobials agents used in treatment of Vibrio sp. infections[27,28]. As an attempt to further explore its an- timicrobial resistance traits, this strain was selected for genome sequencing. Data description Genomic DNA of Vibrio sp. SALL 6 was extracted us- ing MasterpureTM DNA purification kit (Epicentre, Il lumina Inc., Madison, WI, USA) before performing RNase (Qiagen, USA) treatment[29,30]. The DNA qual- ity was quantified using NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA). Illumina sequencing library of genomic DNA was prepared using NexteraTM DNA Sample Prep- aration kit (Illumina, San Diego, CA, USA) and library quality was validated by a Bioanalyzer 2100 high sen- sitivity DNA kit (Agilent Technologies, Palo Alto, CA) prior to sequencing. The genome of SALL 6 strain was sequenced on MiSeq platform with MiSeq Reagent Kit 2 (2 x 250bp; Illumina Inc, San Diego, CA, USA)[31]. The trimmed sequences were de novo assembled with CLC Genomic Workbench version 5.1 (CLC Bio, Denmark). Contigs with at least 200 bp and 30-fold coverage were selected for gene prediction and annotation. The bacte- ria identity was also checked by local BLAST against NCBI prokaryotic 16S rRNA database. Bacteria gene coding sequence (CDS) was predicted from the draft ge- nome using Prodigal (version 2.6.1)[32]. Gene annotation was performed by local BLAST of translated predicted CDS against NCBI-nr database and also on Rapid An- notation using Subsystem Technology (RAST) server[33]. Presence of rRNA and tRNA genes were detected using RNAmmer and tRNAscan SE version 1.21[34,35] A total of 81 contigs were generated with N50 size of 193,737 bp. The assembled genome size of Vibrio sp. SALL 6 contains 4,989,632 bp, with an average genome coverage of 54- fold with a G + C content of 45.4 % (Table 1). The whole genome project was deposited at DDBJ/EMBL/GenBank under accession MQVK00000000. The version described in this paper is the first version MQVK01000000. It is composed of 81 contigs and there were 4,500 protein cod- ing genes (out of a total of 4,681 predicted gene) (Table 1). Table 1. General features of Vibrio sp. SALL 6 draft genome Attribute Value Genome size (bp) 4,989,632 G + C content % 45.4 DNA scaffold 81 Total genes 4,681 Protein coding genes 4,500 RNA genes (5S, 16S, 24S) 2, 6, 1 Pseudo genes 66 The analysis obtained from RAST server revealed 544 subsystems (Figure 1). The annotated genome has 74 genes responsible for resistance to antibiotic and toxic compounds including 28 genes for multidrug resistance efflux pumps, one gene for beta-lactamase, four genes for resistance to fluoroquinolones, and two genes for tetra- cycline resistance. The phenotypic resistance shown by Vibrio sp. SALL 6 toward ampicillin and cefotaxime is closely related to the gene coding beta-lactamase in the genome. Multidrug resistance profile seen in the phenotype and genes of Vibrio sp. SALL 6 genome illustrates how ex- tensive antibiotics have been utilized in agriculture and aquaculture settings. The efficacy of clinical antibiot- ics are declining, thus there is a need for non-antibiotic method such as bacteriophage application or natural plant antimicrobials to manage Vibrio infections in the aqua- culture[36,37]. Genome squence of Vibrio... Figure 1. Subsystem category distribution of Vibrio sp. SALL 6 (based on RAST annotation server 3 Conflict of Interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Acknowledgement This work was supported by University of Malaya for High Impact Research Grant (UM-MOHE HIR Nature Micro- biome Grant No. H-50001-A000027 and No. A000001- 50001) and PPP Grant (PG090-2015B) awarded to K-GC. Reference 1. Elmahdi S, DaSilva LV, and Parveen S. Antibiotic resistance of Vibrio parahaemolyticus and Vibrio vulnificus in various countries: A review. Food Microbiol, 2016; 57: 128–134. 2. 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