ABSTRACT
Vibrio parahaemolyticus is a clinically significant marine bacterium implicated in gastroenteritis among consumers of raw or undercooked seafood. This report presents the whole-genome sequence of a unique strain of V. parahaemolyticus isolated from oysters harvested in Canada.
GENOME ANNOUNCEMENT
Vibrio parahaemolyticus is autochthonous in estuarine environments around the world and is detected in seafood from contaminated harvest sites. Since the 1950s, V. parahaemolyticus has been frequently implicated in cases of seafood-borne gastroenteritis and other related illnesses (1, 2). Most of the clinical isolates are known to express thermostable direct hemolysin (TDH) and/or TDH-related hemolysin (TRH), encoded by tdh and trh, respectively (1, 3, 4). However, clinical isolates lacking both tdh and trh, as confirmed by PCR, have been detected from several regions, including in recent years from Canada (5) and from the United States (6). The diversity and dynamics of V. parahaemolyticus strains testify to the adaptability of the species to a wide range of habitat and/or environmental challenges by virtue of its genome plasticity and resultant evolution (7). Changes can also occur via the processes of integration and/or conjugation of genetic material through horizontal transfer (8). These events can lead to the emergence of new pathogenic strains as well as evolution of the existing pathogens (7, 9).
Knowledge of the global distribution and epidemiology of V. parahaemolyticus, including its genomic profile, will help understand its impact on the human host and the marine environment. Here, we report the genomic sequence of an environmental V. parahaemolyticus isolate from oysters harvested in Canada in the summer of 2005 and sourced to Ladysmith Harbor, British Columbia, Canada.
V. parahaemolyticus strain S107-1 was isolated and characterized at the Health Canada laboratory by an in-house procedure, the details of which have been published elsewhere (10). An antimicrobial resistance profile (AMR) of the isolate was determined by Kirby-Bauer's disk diffusion method (11, 12). Whole-genome sequencing of V. parahaemolyticus S107-1 containing ICEVpaCan1 was carried out from genomic DNA extracted from 2 ml of exponential-phase culture using the Gentra Puregene kit (Qiagen). PacBio RS II single-molecule real-time sequencing (PacBio SMRTcell) and de novo genome assembly were performed at the McGill University and Génome Québec Innovation Centre with the HGAP version 3 method. Annotation data for V. parahaemolyticus S107-1 were provided by the NCBI Prokaryotic Genome Annotation Pipeline (13).
Biochemical analysis using API20E diagnostic strips confirmed the isolate (S107-1) to be V. parahaemolyticus, which also tested positive by PCR for the presence of the species-specific marker, thermolabile hemolysin gene (tlh), while the known virulence markers (tdh and trh) for V. parahaemolyticus tested negative by PCR. This isolate was resistant to three antibiotics, ampicillin, streptomycin, and cephalothin, and showed intermediate resistance to piperacillin and kanamycin. Whole-genome sequencing analysis identified and assembled the two chromosomes of sizes 3,445,421 bp and 1,757,905 bp for chromosomes I and II, respectively.
The presence of an integrative and conjugative element (ICE), consequently named ICEVpaCan1, was detected at the 5ʹ end of the prfC gene on chromosome I of the V. parahaemolyticus isolate S107-1. This element of the SXT/R391 family has a size of 81,255 bp and does not carry any predicted resistance genes.
Accession number(s).
The complete genome sequences of the two chromosomes of V. parahaemolyticus strain S107-1 were deposited at GenBank under accession numbers CP028481 (chromosome I) and CP028482 (chromosome II).
ACKNOWLEDGMENTS
This work was funded (A-base) by Health Canada to support Canada’s Food Safety Programs, and the subsequent molecular analyses were pursued at the Burrus Laboratory, University of Sherbrooke, Sherbrooke, Quebec, Canada. This work was also supported by a discovery grant (2016-04365) from the Natural Sciences and Engineering Council of Canada (NSERC) and a project grant (PJT-153071) from the Canadian Institutes of Health Research (CIHR) to V.B.
Footnotes
Citation Bioteau A, Huguet K, Burrus V, Banerjee S. 2018. Genome sequence of a Canadian Vibrio parahaemolyticus isolate with unique mobilizing capacity. Genome Announc 6:e00520-18. https://doi.org/10.1128/genomeA.00520-18.
REFERENCES
- 1.Ceccarelli D, Hasan NA, Huq A, Colwell RR. 2013. Distribution and dynamics of epidemic and pandemic Vibrio parahaemolyticus virulence factors. Front Cell Infect Microbiol 3:97. doi: 10.3389/fcimb.2013.00097. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Morris JG Jr, Acheson D. 2003. Cholera and other types of vibriosis: a story of human pandemics and oyster on the half shell. Clin Infect Dis 37:272–280. doi: 10.1086/375600. [DOI] [PubMed] [Google Scholar]
- 3.Nishibuchi M, Fasano A, Russell RG, Kaper JB. 1992. Enterotoxigenicity of Vibrio parahaemolyticus with and without genes encoding thermostable direct hemolysin. Infect Immun 60:3539–3545. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Honda T, Ni YX, Miwatani T. 1988. Purification and characterization of a hemolysin produced by a clinical isolate of Kanagawa phenomenon-negative Vibrio parahaemolyticus and related to the thermostable direct hemolysin. Infect Immun 56:961–965. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Banerjee SK, Kearney AK, Nadon CA, Peterson C-L, Tyler K, Bakouche L, Clark CG, Hoang L, Gilmour MW, Farber JM. 2014. Phenotypic and genotypic characterization of Canadian clinical isolates of Vibrio parahaemolyticus collected from 2000 to 2009. J Clin Microbiol 52:1081–1088. doi: 10.1128/JCM.03047-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Jones JL, Lüdeke CHM, Bowers JC, Garrett N, Fischer M, Parsons MB, Bopp CA, DePaola A. 2012. Biochemical, serological and virulence characterization of clinical and oyster Vibrio parahaemolyticus isolates. J Clin Microbiol 50:2343–2352. doi: 10.1128/JCM.00196-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Haley BJ, Kokashvili T, Tskshvediani A, Janelidze N, Mitaishvili N, Grim CJ, Constantin de Magny G, Chen AJ, Taviani E, Eliashvili T, Tediashvili M, Whitehouse CA, Colwell RR, Huq A. 2014. Molecular diversity and predictability of Vibrio parahaemolyticus along the Georgian coastal zone of the Black Sea. Front Microbiol 5:45. doi: 10.3389/fmicb.2014.00045. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Burrus V, Waldor MK. 2004. Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155:376–386. doi: 10.1016/j.resmic.2004.01.012. [DOI] [PubMed] [Google Scholar]
- 9.Espejo RT, García K, Plaza N. 2017. Insight into the origin and evolution of the Vibrio parahaemolyticus pandemic strain. Front Microbiol 8:1397. doi: 10.3389/fmicb.2017.01397. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Banerjee SK, Farber JM. 2017. Detection, enumeration and isolation of Vibrio parahaemolyticus and V. vulnificus from seafood: development of a multidisciplinary protocol. J AOAC Int 100:445–453. doi: 10.5740/jaoacint.16-0290. [DOI] [PubMed] [Google Scholar]
- 11.Bauer AW, Kirby WMM, Sherris JC, Turck M. 1966. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496. doi: 10.1093/ajcp/45.4_ts.493. [DOI] [PubMed] [Google Scholar]
- 12.Clinical and Laboratory Standards Institute (CLSI). 2013. Performance standards for antimicrobial susceptibility testing; 23rd informational supplement. CLSI document, M100-S23 Clinical and Laboratory Standards Institute, Wayne, PA. [Google Scholar]
- 13.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki E, Zaslavsky L, Lomsadze A, Pruitt K, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]