Abstract
Vibrio parahaemolyticus is the leading bacterial pathogen associated with seafood consumption. Here, we report the draft genome sequences of one marine and one clinical strain, both isolated in Sweden. These sequences will inform future comparative analysis of V. parahaemolyticus in northern Europe.
GENOME ANNOUNCEMENT
Vibrio parahaemolyticus is a Gram-negative marine bacterium that may live freely or attached to abiotic or biotic surfaces. The majority of marine strains are apathogenic; however, some strains may cause gastroenteritis, often associated with consumption of raw or undercooked shellfish. Clinical isolates frequently carry virulence-associated genes such as the thermostable direct hemolysin (tdh) and tdh-related hemolysin (trh) (1).
In northern Europe, ocean warming is related to a recent increase in V. parahaemolyticus infections (2). Further, travel to and from destinations where V. parahaemolyticus is endemic may lead to increased reporting of clinical cases at Swedish wards. And more generally, globalization (e.g., increased travel and commerce) may lead to the introduction of virulent strains in the local environment, made more hospitable by ocean warming.
Given the emerging risk of V. parahaemolyticus in northern Europe, we sequenced a marine and a clinical strain isolated in Sweden. The marine strain was isolated from the edible blue mussel, Mytilus edulis, collected outside Sven Lovéns Center for Marine Infrastructure on the Swedish west coast. This marine strain lacks the tdh and trh genes, but it does harbor the σ-VPH hemolysin gene (3). According to an established 7-loci multilocus sequence typing (MLST) scheme (4), this strain has a unique recA allele (no. 338) and therefore represents a new sequence type (ST1579). The clinical strain was isolated at the central hospital of Karlskrona from a male patient who recently returned to Sweden from vacation in Thailand. This clinical strain was tdh+ and shared the same MLST (ST3) as the pandemic complex.
Late log-phase cultures were grown overnight in tryptic soy broth at 30°C with shaking (100 rpm) (Becton, Dickinson, Heidelberg, Germany). Genomic DNA was isolated using a ChargeSwitch gDNA mini bacterial kit per the manufacturer’s instructions (Life Technologies, Carlsbad, CA, USA). DNA was quantified using a BioPhotometer D30 (Eppendorf, Hamburg, Germany) and stored at −20°C. Sequencing of the marine (KVp10) and clinical (Klin) isolates was completed using the Illumina MiSeq platform, at 100× and 75× coverage, respectively. Reads (2 × 300 bp) were trimmed using TrimGalore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to remove adapter sequences and low-quality bases. Overlapping paired reads were merged using FLASH (5). Optimal k-mer size was determined using KmerGenie (6), and reads were assembled de novo using Velvet (7). Draft genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (8), and preliminary analysis was conducted using the SEED Viewer (http://theSEED.org). Both draft genomes share greater than 97% average nucleotide identity with the closed reference genome V. parahaemolyticus RIMD2210633 (9), as determined by JSpecies (10). A more detailed analysis of these draft genomes will be the focus of a future publication.
Accession number(s).
The whole-genome shotgun projects have been deposited at DDBJ/ENA/GenBank under the accession numbers MBTR00000000 (KVp10) and MDTV00000000 (Klin). Additionally, the sequence and profile definitions for each isolate have been deposited in the V. parahaemolyticus MLST database (http://pubmlst.org/vparahaemolyticus).
ACKNOWLEDGMENTS
We thank the Microbiology Laboratory at the Karlskrona Hospital for providing the Swedish clinical isolate, and we thank Rohinee Paranjpye and Gladys Yanagida at NOAA’s Northwest Fisheries Science Center (NWFSC) for assistance in the laboratory. We also thank Narjol Gonzalez-Escalona at the Federal Drug Administration’s Center for Food Safety and Applied Nutrition (FDA-CFSAN) for adding these isolates to the MLST database.
Funding Statement
This study was partly supported by foundations managed by The Royal Swedish Academy of Science. Royal Swedish Academy of Science provided funding to Betty Collin from the P.E. Lindahls fund.
Footnotes
Citation Collin B, Pinnell LJ, Tallman JJ, Turner JW. 2016. Draft genome sequences of one marine and one clinical Vibrio parahaemolyticus strain, both isolated in Sweden. Genome Announc 4(5):e01196-16 doi:10.1128/genomeA.01196-16.
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