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As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile.

Hargreaves KR, Otieno JR, Thanki A, Blades MJ, Millard AD, Browne HP, Lawley TD, Clokie MR - Genome Biol Evol (2015)

Bottom Line: These include ribotypes which are associated with disease, as well as those that are less commonly isolated from patients.In this study, draft genomes have been generated for 13 C. difficile isolates from estuarine sediments including clinically relevant and environmental associated types.In conclusion, estuarine sediments are a source of genetically diverse C. difficile strains with a complex network of prophages, which could contribute to the emergence of new strains in clinics.

View Article: PubMed Central - PubMed

Affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom Department of Ecology and Evolutionary Biology, University of Arizona.

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Prophage sequence present across environmental isolates. Composite genome comparison figure generated using BRIG from performing a BLASTn analysis. Rings correspond to each draft genome sequence input for the 13 isolates, CD196 and M120 in the same order as figure 1. The reference sequences used is a multi-FASTA containing genome sequence of the published temperate phage genomes which are shown in alternative red and blue segments in the outermost ring. Color of the ring indicates ribotype and intensity the sequence similarities. Of the 15 genomes searched, 14 have similarity across the lengths of the medium-sized myoviruses, ΦCD119, φC2, and phiCDHM1. In contrast, fewer isolates have sequence similar to the long tailed myoviruses, and the small myovirus and least to each siphovirus. Patterns of the similarity illustrate the conservation of specific regions of the phage genomes, for example, there is less conservation in the structural gene region (at the 3′-end of the genome) of ΦCD119 compared with φC2.
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evv094-F2: Prophage sequence present across environmental isolates. Composite genome comparison figure generated using BRIG from performing a BLASTn analysis. Rings correspond to each draft genome sequence input for the 13 isolates, CD196 and M120 in the same order as figure 1. The reference sequences used is a multi-FASTA containing genome sequence of the published temperate phage genomes which are shown in alternative red and blue segments in the outermost ring. Color of the ring indicates ribotype and intensity the sequence similarities. Of the 15 genomes searched, 14 have similarity across the lengths of the medium-sized myoviruses, ΦCD119, φC2, and phiCDHM1. In contrast, fewer isolates have sequence similar to the long tailed myoviruses, and the small myovirus and least to each siphovirus. Patterns of the similarity illustrate the conservation of specific regions of the phage genomes, for example, there is less conservation in the structural gene region (at the 3′-end of the genome) of ΦCD119 compared with φC2.

Mentions: The BRIG analysis shows that there are sequences throughout each draft genome that are similar to known C. difficile phages, with the exceptions of the two siphoviruses ΦCD6356 and φCD38-2 (fig. 2). It is important to note that the C. difficile phages vary according to their genetic relatedness, which is often reflected by their particle morphology, see review (Hargreaves and Clokie 2014). In brief, the myoviruses can be grouped into the medium myoviruses, which are ΦCD119, φC2 and phiCDHM1 with genome sizes approximately 53–56 kb, capsid diameters approximately 50–60 nm and contractile tails of approximately 100–110 nm (Goh, Riley, et al. 2005; Govind et al. 2006; Hargreaves, Kropinski, et al. 2014); the long-tailed myoviruses, ϕCD27 and ΦMMP02, with genomes approximately 50–52 kb, capsid diameters of 60–65 nm and tail lengths of 210–258 nm (Mayer et al. 2008; Meessen-Pinard et al. 2012); and small myoviruses which is represented by ΦMMP04 with a genome of approximately 32 kb, capsid of approximately 58 nm and tail length of approximately 106 nm (Meessen-Pinard et al. 2012). The siphoviruses are distinct from the myoviruses as well as to one another, with ΦCD6356 has a genome size of approximately 38 kb, capsid diameter or approximately 64 nm and tail length of approximately 272 nm (Horgan et al. 2010) and φCD38-2 has a 41 kb genome, with a capsid diameter of approximately 60 nm and tail length of approximately 210 nm (Sekulovic et al. 2011).Fig. 2.—


As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile.

Hargreaves KR, Otieno JR, Thanki A, Blades MJ, Millard AD, Browne HP, Lawley TD, Clokie MR - Genome Biol Evol (2015)

Prophage sequence present across environmental isolates. Composite genome comparison figure generated using BRIG from performing a BLASTn analysis. Rings correspond to each draft genome sequence input for the 13 isolates, CD196 and M120 in the same order as figure 1. The reference sequences used is a multi-FASTA containing genome sequence of the published temperate phage genomes which are shown in alternative red and blue segments in the outermost ring. Color of the ring indicates ribotype and intensity the sequence similarities. Of the 15 genomes searched, 14 have similarity across the lengths of the medium-sized myoviruses, ΦCD119, φC2, and phiCDHM1. In contrast, fewer isolates have sequence similar to the long tailed myoviruses, and the small myovirus and least to each siphovirus. Patterns of the similarity illustrate the conservation of specific regions of the phage genomes, for example, there is less conservation in the structural gene region (at the 3′-end of the genome) of ΦCD119 compared with φC2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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evv094-F2: Prophage sequence present across environmental isolates. Composite genome comparison figure generated using BRIG from performing a BLASTn analysis. Rings correspond to each draft genome sequence input for the 13 isolates, CD196 and M120 in the same order as figure 1. The reference sequences used is a multi-FASTA containing genome sequence of the published temperate phage genomes which are shown in alternative red and blue segments in the outermost ring. Color of the ring indicates ribotype and intensity the sequence similarities. Of the 15 genomes searched, 14 have similarity across the lengths of the medium-sized myoviruses, ΦCD119, φC2, and phiCDHM1. In contrast, fewer isolates have sequence similar to the long tailed myoviruses, and the small myovirus and least to each siphovirus. Patterns of the similarity illustrate the conservation of specific regions of the phage genomes, for example, there is less conservation in the structural gene region (at the 3′-end of the genome) of ΦCD119 compared with φC2.
Mentions: The BRIG analysis shows that there are sequences throughout each draft genome that are similar to known C. difficile phages, with the exceptions of the two siphoviruses ΦCD6356 and φCD38-2 (fig. 2). It is important to note that the C. difficile phages vary according to their genetic relatedness, which is often reflected by their particle morphology, see review (Hargreaves and Clokie 2014). In brief, the myoviruses can be grouped into the medium myoviruses, which are ΦCD119, φC2 and phiCDHM1 with genome sizes approximately 53–56 kb, capsid diameters approximately 50–60 nm and contractile tails of approximately 100–110 nm (Goh, Riley, et al. 2005; Govind et al. 2006; Hargreaves, Kropinski, et al. 2014); the long-tailed myoviruses, ϕCD27 and ΦMMP02, with genomes approximately 50–52 kb, capsid diameters of 60–65 nm and tail lengths of 210–258 nm (Mayer et al. 2008; Meessen-Pinard et al. 2012); and small myoviruses which is represented by ΦMMP04 with a genome of approximately 32 kb, capsid of approximately 58 nm and tail length of approximately 106 nm (Meessen-Pinard et al. 2012). The siphoviruses are distinct from the myoviruses as well as to one another, with ΦCD6356 has a genome size of approximately 38 kb, capsid diameter or approximately 64 nm and tail length of approximately 272 nm (Horgan et al. 2010) and φCD38-2 has a 41 kb genome, with a capsid diameter of approximately 60 nm and tail length of approximately 210 nm (Sekulovic et al. 2011).Fig. 2.—

Bottom Line: These include ribotypes which are associated with disease, as well as those that are less commonly isolated from patients.In this study, draft genomes have been generated for 13 C. difficile isolates from estuarine sediments including clinically relevant and environmental associated types.In conclusion, estuarine sediments are a source of genetically diverse C. difficile strains with a complex network of prophages, which could contribute to the emergence of new strains in clinics.

View Article: PubMed Central - PubMed

Affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom Department of Ecology and Evolutionary Biology, University of Arizona.

Show MeSH
Related in: MedlinePlus