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Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates
Between 1996 and 2006, the US Centers for Disease Control reported that the only category of food-borne infections increasing in frequency were those caused by members of the genus Vibrio. The Gram-negative bacterium Vibrio vulnificus is a ubiquitous inhabitant of estuarine waters, and is the number...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360785/ https://www.ncbi.nlm.nih.gov/pubmed/22662170 http://dx.doi.org/10.1371/journal.pone.0037553 |
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author | Morrison, Shatavia S. Williams, Tiffany Cain, Aurora Froelich, Brett Taylor, Casey Baker-Austin, Craig Verner-Jeffreys, David Hartnell, Rachel Oliver, James D. Gibas, Cynthia J. |
author_facet | Morrison, Shatavia S. Williams, Tiffany Cain, Aurora Froelich, Brett Taylor, Casey Baker-Austin, Craig Verner-Jeffreys, David Hartnell, Rachel Oliver, James D. Gibas, Cynthia J. |
author_sort | Morrison, Shatavia S. |
collection | PubMed |
description | Between 1996 and 2006, the US Centers for Disease Control reported that the only category of food-borne infections increasing in frequency were those caused by members of the genus Vibrio. The Gram-negative bacterium Vibrio vulnificus is a ubiquitous inhabitant of estuarine waters, and is the number one cause of seafood-related deaths in the US. Many V. vulnificus isolates have been studied, and it has been shown that two genetically distinct subtypes, distinguished by 16S rDNA and other gene polymorphisms, are associated predominantly with either environmental or clinical isolation. While local genetic differences between the subtypes have been probed, only the genomes of clinical isolates have so far been completely sequenced. In order to better understand V. vulnificus as an agent of disease and to identify the molecular components of its virulence mechanisms, we have completed whole genome shotgun sequencing of three diverse environmental genotypes using a pyrosequencing approach. V. vulnificus strain JY1305 was sequenced to a depth of 33×, and strains E64MW and JY1701 were sequenced to lesser depth, covering approximately 99.9% of each genome. We have performed a comparative analysis of these sequences against the previously published sequences of three V. vulnificus clinical isolates. We find that the genome of V. vulnificus is dynamic, with 1.27% of genes in the C-genotype genomes not found in the E- genotype genomes. We identified key genes that differentiate between the genomes of the clinical and environmental genotypes. 167 genes were found to be specifically associated with environmental genotypes and 278 genes with clinical genotypes. Genes specific to the clinical strains include components of sialic acid catabolism, mannitol fermentation, and a component of a Type IV secretory pathway VirB4, as well as several other genes with potential significance for human virulence. Genes specific to environmental strains included several that may have implications for the balance between self-preservation under stress and nutritional competence. |
format | Online Article Text |
id | pubmed-3360785 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-33607852012-06-01 Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates Morrison, Shatavia S. Williams, Tiffany Cain, Aurora Froelich, Brett Taylor, Casey Baker-Austin, Craig Verner-Jeffreys, David Hartnell, Rachel Oliver, James D. Gibas, Cynthia J. PLoS One Research Article Between 1996 and 2006, the US Centers for Disease Control reported that the only category of food-borne infections increasing in frequency were those caused by members of the genus Vibrio. The Gram-negative bacterium Vibrio vulnificus is a ubiquitous inhabitant of estuarine waters, and is the number one cause of seafood-related deaths in the US. Many V. vulnificus isolates have been studied, and it has been shown that two genetically distinct subtypes, distinguished by 16S rDNA and other gene polymorphisms, are associated predominantly with either environmental or clinical isolation. While local genetic differences between the subtypes have been probed, only the genomes of clinical isolates have so far been completely sequenced. In order to better understand V. vulnificus as an agent of disease and to identify the molecular components of its virulence mechanisms, we have completed whole genome shotgun sequencing of three diverse environmental genotypes using a pyrosequencing approach. V. vulnificus strain JY1305 was sequenced to a depth of 33×, and strains E64MW and JY1701 were sequenced to lesser depth, covering approximately 99.9% of each genome. We have performed a comparative analysis of these sequences against the previously published sequences of three V. vulnificus clinical isolates. We find that the genome of V. vulnificus is dynamic, with 1.27% of genes in the C-genotype genomes not found in the E- genotype genomes. We identified key genes that differentiate between the genomes of the clinical and environmental genotypes. 167 genes were found to be specifically associated with environmental genotypes and 278 genes with clinical genotypes. Genes specific to the clinical strains include components of sialic acid catabolism, mannitol fermentation, and a component of a Type IV secretory pathway VirB4, as well as several other genes with potential significance for human virulence. Genes specific to environmental strains included several that may have implications for the balance between self-preservation under stress and nutritional competence. Public Library of Science 2012-05-25 /pmc/articles/PMC3360785/ /pubmed/22662170 http://dx.doi.org/10.1371/journal.pone.0037553 Text en Morrison et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Morrison, Shatavia S. Williams, Tiffany Cain, Aurora Froelich, Brett Taylor, Casey Baker-Austin, Craig Verner-Jeffreys, David Hartnell, Rachel Oliver, James D. Gibas, Cynthia J. Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates |
title | Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates |
title_full | Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates |
title_fullStr | Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates |
title_full_unstemmed | Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates |
title_short | Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates |
title_sort | pyrosequencing-based comparative genome analysis of vibrio vulnificus environmental isolates |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360785/ https://www.ncbi.nlm.nih.gov/pubmed/22662170 http://dx.doi.org/10.1371/journal.pone.0037553 |
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