title: Genomic diversity of necrotic enteritis-associated strains of Clostridium perfringens: a review.
abstract: The investigation of genomic variation between Clostridium perfringens isolates from poultry has been an important tool to enhance our understanding of the genetic basis of strain pathogenicity and the epidemiology of virulent and avirulent strains within the context of necrotic enteritis (NE). The earliest studies used whole genome profiling techniques such as pulsed-field gel electrophoresis to differentiate isolates and determine their relative levels of relatedness. DNA sequencing has been used to investigate genetic variation in (a) individual genes, such as those encoding the alpha and NetB toxins; (b) panels of housekeeping genes for multi-locus sequence typing and (c) most recently whole genome sequencing to build a more complete picture of genomic differences between isolates. Conclusions drawn from these studies include: differential carriage of large conjugative plasmids accounts for a large proportion of inter-strain differences; plasmid-encoded genes are more highly conserved than chromosomal genes, perhaps indicating a relatively recent origin for the plasmids; isolates from NE-affected birds fall into three distinct sequence-based clades while non-pathogenic isolates from healthy birds tend to be more genomically diverse. Overall, the NE causing strains are closely related to C. perfringens isolates from other birds and other diseases whereas the non-pathogenic poultry strains are generally more remotely related to either the pathogenic strains or the strains from other birds. Genomic analysis has indicated that genes in addition to netB are associated with NE pathogenic isolates. Collectively, this work has resulted in a deeper understanding of the pathogenesis of this important poultry disease.
authors.affiliation: a Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton , Australia.|b Poultry Cooperative Research Centre , University of New England , Armidale , Australia.|c Australian Animal Health Laboratory , CSIRO , Geelong , Australia.
authors.forename: Jake A
authors.initials: JA
authors.lastname: Lacey
authors.affiliation: a Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton , Australia.
authors.forename: Priscilla A
authors.initials: PA
authors.lastname: Johanesen
authors.affiliation: a Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton , Australia.
authors.forename: Dena
authors.initials: D
authors.lastname: Lyras
authors.affiliation: a Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton , Australia.|b Poultry Cooperative Research Centre , University of New England , Armidale , Australia.|c Australian Animal Health Laboratory , CSIRO , Geelong , Australia.|d School of Science , RMIT University , Bundoora , Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Moore
mesh_terms: D000818:Animals; D001427:Bacterial Toxins / Q000235:genetics; D015373:Bacterial Typing Techniques / Q000662:veterinary; D002876:Chromosomes, Bacterial / Q000235:genetics; D003015:Clostridium Infections / Q000382:microbiology / Q000662:veterinary*; D003016:Clostridium perfringens / Q000235:genetics* / Q000302:isolation & purification; D016521:Electrophoresis, Gel, Pulsed-Field / Q000662:veterinary; D004751:Enteritis / Q000382:microbiology / Q000662:veterinary*; D004768:Enterotoxins / Q000235:genetics; D014644:Genetic Variation; D023281:Genomics; D058885:Multilocus Sequence Typing / Q000662:veterinary; D010957:Plasmids / Q000235:genetics; D011200:Poultry / Q000382:microbiology*; D011201:Poultry Diseases / Q000382:microbiology*
chemical_list: D001427:Bacterial Toxins; D004768:Enterotoxins
keywords: Clostridium perfringens; MLST; MLVA; Necrotic enteritis; PFGE; chicken; comparative genomics; netB