Draft Genome Sequence of Israeli Outbreak-Associated Vibrio vulnificus Biotype 3 Clinical Isolate BAA87

Phillips, Kelsey E.; Schipma, Matthew J.; Satchell, K.J.F.

doi:10.1128/genomea.00032-14

“…The five Israeli samples—three human pathogenic biotype 3 strains and two environmental biotype 1 strains—were subjected to QUAST (Gurevich et al, 2013 ), a quality assessment tool for genome assemblies, using CMCP6 as a reference genome. We used the assembled genomes of two other biotype 3 strains, BAA87 and VVyb1, which were published by others for comparison purposes (Danin-Poleg et al, 2013 ; Phillips et al, 2014 ). The assembled genomes of biotype 3 strains (VV9-09, 491771, VV 4-03, BAA87, and VVyb1) showed similar characteristics and were different from the environmental strains (2322 and 101/04) (Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships

Koton

¹

,

Gordon

²

,

Chalifa‐Caspi

³

et al. 2015

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In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59 and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C) and environmental (E), all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins) were present in all human pathogenic strains (both biotype 3 and non-biotype 3) and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS) proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and formed a genetically distinct group within the E-cluster. The unique epidemiological circumstances facilitated disease outbreak and brought this genotype to the attention of the scientific community.

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“…The whole-genome sequence of BAA87 (GenBank accession no. JDSE00000000.1) has been published separately (55).…”

Section: Methodsmentioning

confidence: 99%

Vibrio vulnificus Biotype 3 Multifunctional Autoprocessing RTX Toxin Is an Adenylate Cyclase Toxin Essential for Virulence in Mice

Ziolo

¹

,

Jeong

²

,

Kwak

³

et al. 2014

Self Cite

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Vibrio vulnificus is an environmental organism that causes both food-borne and wound infections with high morbidity and mortality in humans. The annual incidence and global distribution of infections associated with this pathogen are increasing with climate change. In the late 1990s, an outbreak of tilapia-associated wound infections in Israel was linked to a previously unrecognized variant of V. vulnificus designated biotype 3. The sudden emergence and clonality of the outbreak suggest that this strain may be a true newly emergent pathogen with novel virulence properties compared to those of other V. vulnificus strains. In a subcutaneous infection model to mimic wound infection, the multifunctional autoprocessing RTX (MARTX) toxin of biotype 3 strains was shown to be an essential virulence factor contributing to highly inflammatory skin wounds with severe damage affecting every tissue layer. We conducted a sequencing-based analysis of the MARTX toxin and found that biotype 3 MARTX toxin has an effector domain structure distinct from that of either biotype 1 or biotype 2. Of the two new domains identified, a domain similar to Pseudomonas aeruginosa ExoY was shown to confer adenylate cyclase activity on the MARTX toxin. This is the first demonstration that the biotype 3 MARTX toxin is essential for virulence and that the ExoY-like MARTX effector domain is a catalytically active adenylate cyclase.

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“…Nearly 22 and 56% of the core and accessory genomes encoded poorly characterized proteins (including proteins categorized as general function, unknown function, or not in COG database). The average size of the accessory genome of V. vulnificus strain was 1662 kbp (being smallest in the clinical strain ATCC 27562, 781 kbp, and largest in (Danin-Poleg et al, 2013;Phillips et al, 2014 the environmental strain 101/4, 2044 kbp). BLAST alignment of the non-core genomes against the reference clinical strain CMCP6 showed that most of the non-core genomic regions aligned to the large chromosome (data not shown).…”

Section: Core and Accessory Genomesmentioning

confidence: 99%

“…The five Israeli samples-three human pathogenic biotype 3 strains and two environmental biotype 1 strains-were subjected to QUAST (Gurevich et al, 2013), a quality assessment tool for genome assemblies, using CMCP6 as a reference genome. We used the assembled genomes of two other biotype 3 strains, BAA87 and VVyb1, which were published by others for comparison purposes (Danin-Poleg et al, 2013;Phillips et al, 2014). The assembled genomes of biotype 3 strains (VV9-09, 491771, VV 4-03, BAA87, and VVyb1) showed similar characteristics and were different from the environmental strains (2322 and 101/04) ( Table 2).…”

Section: Sequencing Quality and Read Mapping To Reference Genomesmentioning

confidence: 99%

Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships

Bisharat¹

2016

Preprint

0

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In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59 and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C) and environmental (E), all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins) were present in all human pathogenic strains (both biotype 3 and non-biotype 3) and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS) proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and formed a genetically distinct group within the E-cluster. The unique epidemiological circumstances facilitated disease outbreak and brought this genotype to the attention of the scientific community.

show abstract

Draft Genome Sequence of Israeli Outbreak-Associated Vibrio vulnificus Biotype 3 Clinical Isolate BAA87

Cited by 6 publications

References 13 publications

Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships

Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships

Vibrio vulnificus Biotype 3 Multifunctional Autoprocessing RTX Toxin Is an Adenylate Cyclase Toxin Essential for Virulence in Mice

Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships

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