title: As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile.
abstract: The bacterium Clostridium difficile is a significant cause of nosocomial infections worldwide. The pathogenic success of this organism can be attributed to its flexible genome which is characterized by the exchange of mobile genetic elements, and by ongoing genome evolution. Despite its pathogenic status, C. difficile can also be carried asymptomatically, and has been isolated from natural environments such as water and sediments where multiple strain types (ribotypes) are found in close proximity. These include ribotypes which are associated with disease, as well as those that are less commonly isolated from patients. Little is known about the genomic content of strains in such reservoirs in the natural environment. In this study, draft genomes have been generated for 13 C. difficile isolates from estuarine sediments including clinically relevant and environmental associated types. To identify the genetic diversity within this strain collection, whole-genome comparisons were performed using the assemblies. The strains are highly genetically diverse with regards to the C. difficile "mobilome," which includes transposons and prophage elements. We identified a novel transposon-like element in two R078 isolates. Multiple, related and unrelated, prophages were detected in isolates across ribotype groups, including two novel prophage elements and those related to the transducing phage φC2. The susceptibility of these isolates to lytic phage infection was tested using a panel of characterized phages found from the same locality. 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.
authors.affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom Department of Ecology and Evolutionary Biology, University of Arizona.
authors.forename: Katherine R
authors.initials: KR
authors.lastname: Hargreaves
authors.affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
authors.forename: James R
authors.initials: JR
authors.lastname: Otieno
authors.affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom.
authors.forename: Anisha
authors.initials: A
authors.lastname: Thanki
authors.affiliation: Bioinformatics and Biostatistics Analysis Support Hub (BBASH), Core Biotechnology Services, University of Leicester, United Kingdom.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Blades
authors.affiliation: Microbiology & Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Millard
authors.affiliation: Microbial Pathogenesis Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Hilary P
authors.initials: HP
authors.lastname: Browne
authors.affiliation: Microbial Pathogenesis Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Trevor D
authors.initials: TD
authors.lastname: Lawley
authors.affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom mrjc1@le.ac.uk.
authors.forename: Martha R J
authors.initials: MR
authors.lastname: Clokie
mesh_terms: D001427:Bacterial Toxins / Q000235:genetics; D016360:Clostridioides difficile / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity / Q000821:virology; D004783:Environmental Microbiology; D063366:Estuaries; D014644:Genetic Variation; D016680:Genome, Bacterial; D019015:Geologic Sediments / Q000382:microbiology; D039002:Prophages / Q000235:genetics*; D014774:Virulence / Q000235:genetics
chemical_list: D001427:Bacterial Toxins
keywords: Clostridium difficile; bacteriophage; mobilome; pathogen genome evolution; prophage; virulence