Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis
Vibrio parahaemolyticus has been the most common food-borne pathogen in southern China, especially the O3:K6 pandemic clone and its serovariants. Recently, the serotype O4:K8 became more and more prevalent in southern China, which was different from the O3:K6 pandemic clone. Thus, the aim of the pre...
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| creator | Li, Baisheng Yang, Xingfen Tan, Hailing Ke, Bixia He, Dongmei Ke, Changwen Zhang, Yonghui |
| description | Vibrio parahaemolyticus has been the most common food-borne pathogen in southern China, especially the O3:K6 pandemic clone and its serovariants. Recently, the serotype O4:K8 became more and more prevalent in southern China, which was different from the O3:K6 pandemic clone. Thus, the aim of the present work was to elucidate the molecular characteristics of the O4:K8. Some O3:K6 pandemic clone and its serovariants isolated in the same period were selected for comparative analysis, which were still dominant clone locally. The whole genome sequencing (WGS) was applied to characterize 20 strains of V. parahaemolyticus isolated from food-borne diarrheal cases and belonging to the serotype O4:K8, O3:K6 and O1:KUT (untypable), prevalent serotypes in recent southern China. The results showed that all these isolates were positive for the thermostable direct hemolysin gene (tdh), while negative for the TDH-related hemolysin gene (trh). We compared the V. parahaemolyticus strains to those of 31 strains isolated overseas and were available from NCBI genome database. A WGS-SNPs phylogenetic analysis of all the genomes revealed that the strains formed an important genetic lineage, which was genetically distinct from the O3:K6, O1:KUT and other internationals strains. Comparative genome analysis also revealed that all the O4:K8 strains carried the entire T3SS-1 and VpaI-7 (T3SS-2) regions, the most important virulent elements of the O3:K6 pandemic clone. However, all the O4:K8 strains lacked the entire VpaI-1 and VpaI-4 regions and carried only few ORFs of the VpaI-5 and VpaI-6, which were considered to be unique among post-1995 strains belonging to the O3:K6 pandemic clone. Our data showed that the O4:K8 strains possessed the virulence factors similar to the O3:K6 pandemic clone, which may have enabled them to become prevalent in southern China. Our study also revealed that WGS-bases analysis may help improve understanding epidemiology of this bacterium in food-borne disease surveillance.
•We applied WGS to analyze the clinical V. parahaemolyticus O4:K8 in southern China.•WGS-SNPs phylogenetic analysis revealed the O4:K8 strains formed a distinct genetic lineage.•Comparative genome analysis revealed the O4:K8 carried T3SS-1 and T3SS-2 elements.•The WGS-bases analysis improves understanding epidemiology of this bacterium in food-borne disease surveillance. |
| doi_str_mv | 10.1016/j.ijfoodmicro.2017.01.001 |
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•We applied WGS to analyze the clinical V. parahaemolyticus O4:K8 in southern China.•WGS-SNPs phylogenetic analysis revealed the O4:K8 strains formed a distinct genetic lineage.•Comparative genome analysis revealed the O4:K8 carried T3SS-1 and T3SS-2 elements.•The WGS-bases analysis improves understanding epidemiology of this bacterium in food-borne disease surveillance.</description><identifier>ISSN: 0168-1605</identifier><identifier>EISSN: 1879-3460</identifier><identifier>DOI: 10.1016/j.ijfoodmicro.2017.01.001</identifier><identifier>PMID: 28073082</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Bacteria ; Bacterial Toxins - genetics ; Base Sequence ; China - epidemiology ; Comparative analysis ; Diarrhea ; Diarrhea - microbiology ; Disease Outbreaks ; DNA, Bacterial - genetics ; Epidemiology ; Food ; Foodborne Diseases - microbiology ; Gene sequencing ; Genome, Bacterial - genetics ; Genomes ; Gram-negative bacteria ; Hemolysin Proteins - genetics ; Humans ; Nucleotide sequence ; Pandemics ; Pathogens ; Phylogenetic analysis ; Phylogeny ; Sequence Analysis, DNA ; Serogroup ; Serotypes ; Serotyping ; Single-nucleotide polymorphism ; SNPs ; Type III Secretion Systems - genetics ; Vibrio Infections - microbiology ; Vibrio parahaemolyticus ; Vibrio parahaemolyticus - genetics ; Vibrio parahaemolyticus - isolation & purification ; Vibrio parahaemolyticus - pathogenicity ; Virulence ; Virulence factors ; Virulence Factors - genetics ; Waterborne diseases ; Whole genome sequence</subject><ispartof>International journal of food microbiology, 2017-03, Vol.244, p.90-95</ispartof><rights>2017 Elsevier B.V.</rights><rights>Copyright © 2017 Elsevier B.V. All rights reserved.</rights><rights>Copyright Elsevier BV Mar 6, 2017</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c405t-38a0c5087126d57a52900b26bc16683263e6ae05ab33bbc2ab29bacdead1c82b3</citedby><cites>FETCH-LOGICAL-c405t-38a0c5087126d57a52900b26bc16683263e6ae05ab33bbc2ab29bacdead1c82b3</cites><orcidid>0000-0003-1842-316X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ijfoodmicro.2017.01.001$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3548,27922,27923,45993</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28073082$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Baisheng</creatorcontrib><creatorcontrib>Yang, Xingfen</creatorcontrib><creatorcontrib>Tan, Hailing</creatorcontrib><creatorcontrib>Ke, Bixia</creatorcontrib><creatorcontrib>He, Dongmei</creatorcontrib><creatorcontrib>Ke, Changwen</creatorcontrib><creatorcontrib>Zhang, Yonghui</creatorcontrib><title>Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis</title><title>International journal of food microbiology</title><addtitle>Int J Food Microbiol</addtitle><description>Vibrio parahaemolyticus has been the most common food-borne pathogen in southern China, especially the O3:K6 pandemic clone and its serovariants. Recently, the serotype O4:K8 became more and more prevalent in southern China, which was different from the O3:K6 pandemic clone. Thus, the aim of the present work was to elucidate the molecular characteristics of the O4:K8. Some O3:K6 pandemic clone and its serovariants isolated in the same period were selected for comparative analysis, which were still dominant clone locally. The whole genome sequencing (WGS) was applied to characterize 20 strains of V. parahaemolyticus isolated from food-borne diarrheal cases and belonging to the serotype O4:K8, O3:K6 and O1:KUT (untypable), prevalent serotypes in recent southern China. The results showed that all these isolates were positive for the thermostable direct hemolysin gene (tdh), while negative for the TDH-related hemolysin gene (trh). We compared the V. parahaemolyticus strains to those of 31 strains isolated overseas and were available from NCBI genome database. A WGS-SNPs phylogenetic analysis of all the genomes revealed that the strains formed an important genetic lineage, which was genetically distinct from the O3:K6, O1:KUT and other internationals strains. Comparative genome analysis also revealed that all the O4:K8 strains carried the entire T3SS-1 and VpaI-7 (T3SS-2) regions, the most important virulent elements of the O3:K6 pandemic clone. However, all the O4:K8 strains lacked the entire VpaI-1 and VpaI-4 regions and carried only few ORFs of the VpaI-5 and VpaI-6, which were considered to be unique among post-1995 strains belonging to the O3:K6 pandemic clone. Our data showed that the O4:K8 strains possessed the virulence factors similar to the O3:K6 pandemic clone, which may have enabled them to become prevalent in southern China. Our study also revealed that WGS-bases analysis may help improve understanding epidemiology of this bacterium in food-borne disease surveillance.
•We applied WGS to analyze the clinical V. parahaemolyticus O4:K8 in southern China.•WGS-SNPs phylogenetic analysis revealed the O4:K8 strains formed a distinct genetic lineage.•Comparative genome analysis revealed the O4:K8 carried T3SS-1 and T3SS-2 elements.•The WGS-bases analysis improves understanding epidemiology of this bacterium in food-borne disease surveillance.</description><subject>Bacteria</subject><subject>Bacterial Toxins - genetics</subject><subject>Base Sequence</subject><subject>China - epidemiology</subject><subject>Comparative analysis</subject><subject>Diarrhea</subject><subject>Diarrhea - microbiology</subject><subject>Disease Outbreaks</subject><subject>DNA, Bacterial - genetics</subject><subject>Epidemiology</subject><subject>Food</subject><subject>Foodborne Diseases - microbiology</subject><subject>Gene sequencing</subject><subject>Genome, Bacterial - genetics</subject><subject>Genomes</subject><subject>Gram-negative bacteria</subject><subject>Hemolysin Proteins - genetics</subject><subject>Humans</subject><subject>Nucleotide sequence</subject><subject>Pandemics</subject><subject>Pathogens</subject><subject>Phylogenetic analysis</subject><subject>Phylogeny</subject><subject>Sequence Analysis, DNA</subject><subject>Serogroup</subject><subject>Serotypes</subject><subject>Serotyping</subject><subject>Single-nucleotide polymorphism</subject><subject>SNPs</subject><subject>Type III Secretion Systems - genetics</subject><subject>Vibrio Infections - microbiology</subject><subject>Vibrio parahaemolyticus</subject><subject>Vibrio parahaemolyticus - genetics</subject><subject>Vibrio parahaemolyticus - isolation & purification</subject><subject>Vibrio parahaemolyticus - pathogenicity</subject><subject>Virulence</subject><subject>Virulence factors</subject><subject>Virulence Factors - genetics</subject><subject>Waterborne diseases</subject><subject>Whole genome sequence</subject><issn>0168-1605</issn><issn>1879-3460</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkTuP1DAURiMEYoeFv4CMaGgSru2x49ChES-x0jZAa_lxh3GU2IOdgKbkn-PRLAhRUd3invvQd5rmGYWOApUvxy6M-5T8HFxOHQPad0A7AHqv2VDVDy3fSrjfbCqrWipBXDWPShkBQHAOD5srpqDnoNim-fkl2BwSOZpsDgbnNJ2W4NZCbrevPiqyT3kuxJBjWjAuwUzkmNGnOUQTF-KmFJGESEpalwPmSHaH2iGmEI8LugU9sSfy45AmbL9iTDOSgt9WjA6JiWY6lVAeNw_2Zir45K5eN5_fvvm0e9_e3L77sHt907otiKXlyoAToHrKpBe9EWwAsExaR6VUnEmO0iAIYzm31jFj2WCN82g8dYpZft28uOw95lRfKIueQ3E4TSZiWoumSvS92DImKvr8H3RMa67_VmrgkjEGbKjUcKGqhFIy7vUxh9nkk6agz570qP_ypM-eNFBdPdXZp3cXVjuj_zP5W0wFdhcAayTfA2ZdXDjn5kOuwWqfwn-c-QX5QquN</recordid><startdate>20170306</startdate><enddate>20170306</enddate><creator>Li, Baisheng</creator><creator>Yang, Xingfen</creator><creator>Tan, Hailing</creator><creator>Ke, Bixia</creator><creator>He, Dongmei</creator><creator>Ke, Changwen</creator><creator>Zhang, Yonghui</creator><general>Elsevier B.V</general><general>Elsevier BV</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QR</scope><scope>7T7</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-1842-316X</orcidid></search><sort><creationdate>20170306</creationdate><title>Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis</title><author>Li, Baisheng ; Yang, Xingfen ; Tan, Hailing ; Ke, Bixia ; He, Dongmei ; Ke, Changwen ; Zhang, Yonghui</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c405t-38a0c5087126d57a52900b26bc16683263e6ae05ab33bbc2ab29bacdead1c82b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Bacteria</topic><topic>Bacterial Toxins - genetics</topic><topic>Base Sequence</topic><topic>China - epidemiology</topic><topic>Comparative analysis</topic><topic>Diarrhea</topic><topic>Diarrhea - microbiology</topic><topic>Disease Outbreaks</topic><topic>DNA, Bacterial - genetics</topic><topic>Epidemiology</topic><topic>Food</topic><topic>Foodborne Diseases - microbiology</topic><topic>Gene sequencing</topic><topic>Genome, Bacterial - genetics</topic><topic>Genomes</topic><topic>Gram-negative bacteria</topic><topic>Hemolysin Proteins - genetics</topic><topic>Humans</topic><topic>Nucleotide sequence</topic><topic>Pandemics</topic><topic>Pathogens</topic><topic>Phylogenetic analysis</topic><topic>Phylogeny</topic><topic>Sequence Analysis, DNA</topic><topic>Serogroup</topic><topic>Serotypes</topic><topic>Serotyping</topic><topic>Single-nucleotide polymorphism</topic><topic>SNPs</topic><topic>Type III Secretion Systems - genetics</topic><topic>Vibrio Infections - microbiology</topic><topic>Vibrio parahaemolyticus</topic><topic>Vibrio parahaemolyticus - genetics</topic><topic>Vibrio parahaemolyticus - isolation & purification</topic><topic>Vibrio parahaemolyticus - pathogenicity</topic><topic>Virulence</topic><topic>Virulence factors</topic><topic>Virulence Factors - genetics</topic><topic>Waterborne diseases</topic><topic>Whole genome sequence</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Baisheng</creatorcontrib><creatorcontrib>Yang, Xingfen</creatorcontrib><creatorcontrib>Tan, Hailing</creatorcontrib><creatorcontrib>Ke, Bixia</creatorcontrib><creatorcontrib>He, Dongmei</creatorcontrib><creatorcontrib>Ke, Changwen</creatorcontrib><creatorcontrib>Zhang, Yonghui</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of food microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Baisheng</au><au>Yang, Xingfen</au><au>Tan, Hailing</au><au>Ke, Bixia</au><au>He, Dongmei</au><au>Ke, Changwen</au><au>Zhang, Yonghui</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis</atitle><jtitle>International journal of food microbiology</jtitle><addtitle>Int J Food Microbiol</addtitle><date>2017-03-06</date><risdate>2017</risdate><volume>244</volume><spage>90</spage><epage>95</epage><pages>90-95</pages><issn>0168-1605</issn><eissn>1879-3460</eissn><abstract>Vibrio parahaemolyticus has been the most common food-borne pathogen in southern China, especially the O3:K6 pandemic clone and its serovariants. Recently, the serotype O4:K8 became more and more prevalent in southern China, which was different from the O3:K6 pandemic clone. Thus, the aim of the present work was to elucidate the molecular characteristics of the O4:K8. Some O3:K6 pandemic clone and its serovariants isolated in the same period were selected for comparative analysis, which were still dominant clone locally. The whole genome sequencing (WGS) was applied to characterize 20 strains of V. parahaemolyticus isolated from food-borne diarrheal cases and belonging to the serotype O4:K8, O3:K6 and O1:KUT (untypable), prevalent serotypes in recent southern China. The results showed that all these isolates were positive for the thermostable direct hemolysin gene (tdh), while negative for the TDH-related hemolysin gene (trh). We compared the V. parahaemolyticus strains to those of 31 strains isolated overseas and were available from NCBI genome database. A WGS-SNPs phylogenetic analysis of all the genomes revealed that the strains formed an important genetic lineage, which was genetically distinct from the O3:K6, O1:KUT and other internationals strains. Comparative genome analysis also revealed that all the O4:K8 strains carried the entire T3SS-1 and VpaI-7 (T3SS-2) regions, the most important virulent elements of the O3:K6 pandemic clone. However, all the O4:K8 strains lacked the entire VpaI-1 and VpaI-4 regions and carried only few ORFs of the VpaI-5 and VpaI-6, which were considered to be unique among post-1995 strains belonging to the O3:K6 pandemic clone. Our data showed that the O4:K8 strains possessed the virulence factors similar to the O3:K6 pandemic clone, which may have enabled them to become prevalent in southern China. Our study also revealed that WGS-bases analysis may help improve understanding epidemiology of this bacterium in food-borne disease surveillance.
•We applied WGS to analyze the clinical V. parahaemolyticus O4:K8 in southern China.•WGS-SNPs phylogenetic analysis revealed the O4:K8 strains formed a distinct genetic lineage.•Comparative genome analysis revealed the O4:K8 carried T3SS-1 and T3SS-2 elements.•The WGS-bases analysis improves understanding epidemiology of this bacterium in food-borne disease surveillance.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>28073082</pmid><doi>10.1016/j.ijfoodmicro.2017.01.001</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0003-1842-316X</orcidid></addata></record> |
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| ispartof | International journal of food microbiology, 2017-03, Vol.244, p.90-95 |
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| subjects | Bacteria Bacterial Toxins - genetics Base Sequence China - epidemiology Comparative analysis Diarrhea Diarrhea - microbiology Disease Outbreaks DNA, Bacterial - genetics Epidemiology Food Foodborne Diseases - microbiology Gene sequencing Genome, Bacterial - genetics Genomes Gram-negative bacteria Hemolysin Proteins - genetics Humans Nucleotide sequence Pandemics Pathogens Phylogenetic analysis Phylogeny Sequence Analysis, DNA Serogroup Serotypes Serotyping Single-nucleotide polymorphism SNPs Type III Secretion Systems - genetics Vibrio Infections - microbiology Vibrio parahaemolyticus Vibrio parahaemolyticus - genetics Vibrio parahaemolyticus - isolation & purification Vibrio parahaemolyticus - pathogenicity Virulence Virulence factors Virulence Factors - genetics Waterborne diseases Whole genome sequence |
| title | Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis |
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