Progress in Microbes and Molecular Biology Genome Report 1 Genome sequence of Vibrio sp. OULL4 isolated from shellfish Vengadesh Letchumanan1*, Wen-Si Tan2, Wai-Fong Yin3, Kok-Gan Chan3,4 1Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia 2Illumina Singapore Pte Ltd, Woodlands Industrial Park E1, Singapore 3Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 4International Genome Centre, Jiangsu University, Zhenjiang 212013, PR China Abstract: The members of Vibrionaceae family are Gram-negative bacterium are ubiquitous in marine and estuarine environments. This diverse group of bacteria include many pathogenic strains that potentially cause infection to human and aquaculture animals. Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus are among the few recognized as a major, worldwide cause gastroenteritis, particularly in countries where seafood consumption is high. The control of these vibrios has been a hurdle due to the rising numbers of antibiotic resistant strains in the environments. We report the genome sequence of Vibrio sp. OULL4 isolated from shellfish. The availability of this genome sequence will facilitate the study of its antimicrobial traits, as well as add our knowledge of Vibrio sp. diversity and evolution. Keywords: Vibrionaceae; infection; gastroenteritis; antibiotic; genome Received: 27th February 2020 Accepted: 24th March 2020 Published Online: 6th April 2020 Citation: Letchumanan V, Tan W-S, Yin W-F et al. Genome sequence of Vibrio sp. OULL4 isolated from shellfish. Prog Microbe Mol Biol 2020; 3(1): a0000066. https://doi.org/10.3687/pmmb.a0000066 Introduction Seafood production has double over the years to meet the rising consumer demand for seafood. This involuntary action has exposed aquatic animals to bacterial infec- tions[1,2]. This situation gets complicated and worsen by the emergence of resistant Vibrio sp. strains, which ham- pers medical care. Vibrio sp. is a Gram-negative halophilic bacteria that belongs to the Vibrionaceae family[3–8]. They naturally inhabit the aquatic surroundings and associated with aquatic animals for example crustaceans, molluscs and fish[9–13]. The World Health Organization (WHO) has acknowl- edged antibiotic resistance as a public health hazard that affects millions of people worldwide[14]. Due to excessive use of antibiotics in the aquaculture sector, the incidence of resistance accelerated, mostly among foodborne patho- gens such as Vibrio sp.[15–23], Listeria sp.[24–26], and Salmo- nella sp.[27–32]. The resistant foodborne pathogens poses a threat and challenge to drug discovery programmes worldwide[33,34]. Therefore, it is important to continuously monitor and manage the resistant Vibrio sp. in seafood and environments. Vibrio sp. OULL4 strain was isolated from shellfish originated from a supermarket in Selangor, Malaysia. The strain presented a large yellow colony on selective media—thiosulphate citrate bile salt sucrose (TCBS) agar. The antibiotic susceptibility test was performed to determine to resistance phenotype of Vibrio sp. OULL4 strain. The strain was resistant to 11/14 antibiotics tested, namely the ampicillin, ampicillin/sulbactam, 3rd generation cephalosporin (cefotaxime, ceftazidime), aminoglycoside (amikacin, gentamicin, kanamycin), suphamethox/trimethoprim, oxytetracycline, tetracy- cline, and chloramphenicol. This is a worrying scenario as the antibiotic resistant profile exhibited by the strain is among the recommended antibiotics agents used in treatment if Vibrio sp. infection[35–37]. The Vibrio sp. OULL4 strain was selected for genome sequencing to further explore and understand the antibiotic resistant traits. Data description The genomic DNA of Vibrio sp. OULL4 was extracted using MasterpureTM DNA purification kit (Epicentre, Il lumina Inc., Madison, WI, USA) prior to RNase (Qiagen, Copyright @ 2020 by Letchumanan V and HH Publisher. This work under licensed under the Creative Commons Attribution-NonCom- mercial 4.0 International Lisence (CC-BY-NC4.0) *Correspondence: Vengadesh Letchumanan, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia; vengadesh.letchumanan1@monash.edu. 2 USA) treatment[38,39]. The DNA quality was quantified using NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 2.0 fluorom- eter (Life Technologies, Carlsbad, CA, USA). Illumina sequencing library of genomic DNA was prepared us- ing NexteraTM DNA Sample Preparation kit (Illumina, San Diego, CA, USA) and library quality was validated by a Bioanalyzer 2100 high sensitivity DNA kit (Agi- lent Technologies, Palo Alto, CA) prior to sequencing. The genome of OULL4 strain was sequenced on MiSeq platform with MiSeq Reagent Kit 2 (2 x 250bp; Illumina Inc, San Diego, CA, USA)[40]. The trimmed sequences were de novo assembled with CLC Genomic Workbench version 5.1 (CLC Bio, Denmark). Contigs with at least 200bp and 30-fold coverage were selected for gene pre- diction and annotation. The bacteria identity was also checked by local BLAST against NCBI prokaryotic 16S rRNA database. Prodigal (version 2.6.1) was utilized to predict the bacteria gene coding sequence (CDS) from the draft genome[41]. Gene annotation was performed by local BLAST of translated predicted CDS against NCBI-nr database and on Rapid Annotation using Sub- system Technology (RAST) server[42]. Presence of rRNA and tRNA genes were detected using RNAmmer and tRNAscan SE version 1.21[43,44]A total of 59 contigs were generated with N50 size of 201,133bp. The assembled genome size of Vibrio sp. OULL4 contains 4,146,642 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 MQVJ00000000. It is composed of 59 contigs and there were 3,743 protein coding genes (out of a total of 3,898 predicted gene) (Table 1). Table 1. General features of Vibrio sp. OULL4 draft genome. Attribute Value Genome size (bp) 4,146,642 G + C content % 45.4 DNA scaffold 59 Total genes 3,898 Protein coding genes 3,743 RNA genes (5S, 16S, 24S) 5, 3, 1 Pseudo genes 55 The analysis obtained from RAST server revealed 493 subsystems (Figure 1). The annotated genome has 63 genes responsible for resistance to antibiotic and toxic compounds including 25 genes for multidrug resistance efflux pumps, one gene for beta-lactamase, and two genes for tetracycline resistance. The presences of these genes in the genome is closely related to the phenotypic resis- tance exhibited by the strain toward ampicillin, cefotaxi- me, oxytetracycline, and tetracycline. Genome sequence of Vibrio... Figure 1. Subsystem category distribution of Vibrio sp. OULL4 (based on RAST annotation server). Vibrio sp. OULL4 is a multidrug resistant strain—resis- tant to 11/14 antibiotics tested. The resistant phenotype and genes of genome illustrates how extensive antibiot- ics have been used in aquaculture sector. Some of the re- sistance phenotype seen in this strain possibly due to the misuse of permitted antibiotics in Asian aquaculture in- dustry namely tetracycline, quinolone, oxytetracycline, sulphonamide, and trimethoprim[45]. Soon, our depen- dency to antibiotics will eventually deprive the efficacy of clinical antibiotics. We will need to resort to non-anti- biotic approach such as bacteriophage application or nat- ural plant antimicrobials to manage Vibrio infections in the aquaculture[46–50]. We also could adapt quorum sensing method to understand the various signalling molecules of Vibrio sp. These information are useful in the manage- ment of virulence traits[51]. In summary, the application of antibiotics in aquaculture should be reviewed and moni- tored in order to ensure the efficacy of these antibiotics for treatment. Conflict of Interest The authors declare that the research was conducted in 3 Letchumanan V et al. 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 Na- ture Microbiome Grant No. H-50001-A000027 and No. A000001-50001) and PPP Grant (PG090-2015B) award- ed to K-GC. Authors Contributions The research and manuscript writing were performed by VL and W-ST. W-FY and K-GC provided vital guidance and support for the success of the project. The project was founded by VL and K-GC. Reference 1. Tan LT-H, Lee L-H, Goh B-H. The bioprospecting of anti-Vibrio Strep- tomyces species: Prevalence and applications. Prog Microb Mol Biol 2019; 1(1). 2. Hamdan RH, Peng TL, Ong B, et al. Antibiotics resistance of Vibrio spp. isolated from diseased seabass and tilapia in cage culture. 2018. 3. Letchumanan V, Chan K-G, Lee L-H. 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