title: Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus.
abstract: BACKGROUND
  Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinical isolates of V. parahaemolyticus are currently available, but the genome dynamics across the species and virulence potential of environmental strains on a genome-scale have not been described before.
  
  
  RESULTS
  Here we present genome sequences of four V. parahaemolyticus clinical strains from stool samples of patients and five environmental strains in Hong Kong. Phylogenomics analysis based on single nucleotide polymorphisms revealed a clear distinction between the clinical and environmental isolates. A new gene cluster belonging to the biofilm associated proteins of V. parahaemolyticus was found in clincial strains. In addition, a novel small genomic island frequently found among clinical isolates was reported. A few environmental strains were found harboring virulence genes and prophage elements, indicating their virulence potential. A unique biphenyl degradation pathway was also reported. A database for V. parahaemolyticus (http://kwanlab.bio.cuhk.edu.hk/vp) was constructed here as a platform to access and analyze genome sequences and annotations of the bacterium.
  
  
  CONCLUSIONS
  We have performed a comparative genomics analysis of clinical and environmental strains of V. parahaemolyticus. Our analyses could facilitate understanding of the phylogenetic diversity and niche adaptation of this bacterium.
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.forename: Hin-chung
authors.initials: HC
authors.lastname: Wong
authors.forename: Wenyan
authors.initials: W
authors.lastname: Nong
authors.forename: Man Kit
authors.initials: MK
authors.lastname: Cheung
authors.forename: Patrick Tik Wan
authors.initials: PT
authors.lastname: Law
authors.forename: Kai Man
authors.initials: KM
authors.lastname: Kam
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China. hoishankwan@cuhk.edu.hk.
authors.forename: Hoi Shan
authors.initials: HS
authors.lastname: Kwan
mesh_terms: D001713:Biphenyl Compounds / Q000378:metabolism; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D030541:Databases, Genetic; D004777:Environment; D019143:Evolution, Molecular; D005243:Feces / Q000382:microbiology*; D044404:Genomic Islands / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D014736:Vibrio parahaemolyticus / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity*; D014774:Virulence / Q000235:genetics
chemical_list: D001713:Biphenyl Compounds; C010574:biphenyl