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Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens

Lacey, Jake A., Allnutt, Theodore R., Vezina, Ben, Van, Thi Thu Hao, Stent, Thomas, Han, Xiaoyan, Rood, Julian I., Wade, Ben, Keyburn, Anthony L., Seemann, Torsten, Chen, Honglei, Haring, Volker, Johanesen, Priscilla A., Lyras, Dena and Moore, Robert J. 2018, Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens, BMC Genomics, vol. 19, pp. 1-22, doi: 10.1186/s12864-018-4771-1.

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Title Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens
Formatted title Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens
Author(s) Lacey, Jake A.
Allnutt, Theodore R.ORCID iD for Allnutt, Theodore R. orcid.org/0000-0002-1347-3777
Vezina, Ben
Van, Thi Thu Hao
Stent, Thomas
Han, Xiaoyan
Rood, Julian I.
Wade, Ben
Keyburn, Anthony L.
Seemann, Torsten
Chen, Honglei
Haring, Volker
Johanesen, Priscilla A.
Lyras, Dena
Moore, Robert J.
Journal name BMC Genomics
Volume number 19
Article ID 379
Start page 1
End page 22
Total pages 22
Publisher BMC
Place of publication London, England
Publication date 2018-05-22
ISSN 1471-2164
Keyword(s) Adhesion
Capsule
Clostridium perfringens
Genome
Necrotic enteritis
Pangenome
Prophage
Science & Technology
Life Sciences & Biomedicine
Biotechnology & Applied Microbiology
Genetics & Heredity
TOXIN PLASMIDS
STREPTOCOCCUS-PNEUMONIAE
CAPSULAR POLYSACCHARIDES
GENETIC DIVERSITY
CHICKENS
BACTERIOPHAGE
SEQUENCE
DISEASE
NETB
LOCUS
Summary BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome.

RESULTS: Distinct pathogenic clades of necrotic enteritis-causing C. perfringens were identified. They were characterised by variable regions encoded on the chromosome, with predicted roles in capsule production, adhesion, inhibition of related strains, phage integration, and metabolism. Some strains have almost identical genomes, even though they were isolated from different geographic regions at various times, while other highly distant genomes appear to result in similar outcomes with regard to virulence and pathogenesis.

CONCLUSIONS: The high level of diversity in chicken isolates suggests there is no reliable factor that defines a chicken strain of C. perfringens, however, disease-causing strains can be defined by the presence of netB-encoding plasmids. This study reveals that horizontal gene transfer appears to play a significant role in genetic variation of the C. perfringens chromosome as well as the plasmid content within strains.
Language eng
DOI 10.1186/s12864-018-4771-1
Field of Research 06 Biological Sciences
11 Medical And Health Sciences
08 Information And Computing Sciences
HERDC Research category C1 Refereed article in a scholarly journal
Copyright notice ©2018, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30110091

Document type: Journal Article
Collections: School of Medicine
Open Access Collection
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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.