As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile.
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.
Affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom Department of Ecology and Evolutionary Biology, University of Arizona.Show MeSH
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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.—
Affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom Department of Ecology and Evolutionary Biology, University of Arizona.