title: Diversity and Evolution in the Genome of Clostridium difficile.
abstract: Clostridium difficile infection (CDI) is the leading cause of antimicrobial and health care-associated diarrhea in humans, presenting a significant burden to global health care systems. In the last 2 decades, PCR- and sequence-based techniques, particularly whole-genome sequencing (WGS), have significantly furthered our knowledge of the genetic diversity, evolution, epidemiology, and pathogenicity of this once enigmatic pathogen. C. difficile is taxonomically distinct from many other well-known clostridia, with a diverse population structure comprising hundreds of strain types spread across at least 6 phylogenetic clades. The C. difficile species is defined by a large diverse pangenome with extreme levels of evolutionary plasticity that has been shaped over long time periods by gene flux and recombination, often between divergent lineages. These evolutionary events are in response to environmental and anthropogenic activities and have led to the rapid emergence and worldwide dissemination of virulent clonal lineages. Moreover, genome analysis of large clinically relevant data sets has improved our understanding of CDI outbreaks, transmission, and recurrence. The epidemiology of CDI has changed dramatically over the last 15 years, and CDI may have a foodborne or zoonotic etiology. The WGS era promises to continue to redefine our view of this significant pathogen.
authors.affiliation: Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Knight
authors.affiliation: Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia.
authors.forename: Briony
authors.initials: B
authors.lastname: Elliott
authors.affiliation: Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia.
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Chang
authors.affiliation: Marshall Centre for Infectious Diseases and Training, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia.
authors.forename: Timothy T
authors.initials: TT
authors.lastname: Perkins
authors.affiliation: Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia thomas.riley@uwa.edu.au.
authors.forename: Thomas V
authors.initials: TV
authors.lastname: Riley
mesh_terms: D016360:Clostridioides difficile / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D003015:Clostridium Infections / Q000382:microbiology*; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D010802:Phylogeny