Evolutionary dynamics of Clostridium difficile over short and long time scales.
Clostridium difficile has rapidly emerged as the leading cause of antibiotic-associated diarrheal disease, with the transcontinental spread of various PCR ribotypes, including 001, 017, 027 and 078. However, the genetic basis for the emergence of C. difficile as a human pathogen is unclear. Whole genome sequencing was used to analyze genetic variation and virulence of a diverse collection of thirty C. difficile isolates, to determine both macro and microevolution of the species. Horizontal gene transfer and large-scale recombination of core genes has shaped the C. difficile genome over both short and long time scales. Phylogenetic analysis demonstrates C. difficile is a genetically diverse species, which has evolved within the last 1.1-85 million years. By contrast, the disease-causing isolates have arisen from multiple lineages, suggesting that virulence evolved independently in the highly epidemic lineages.
He
Miao
M
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom.
Sebaihia
Mohammed
M
Lawley
Trevor D
TD
Stabler
Richard A
RA
Dawson
Lisa F
LF
Martin
Melissa J
MJ
Holt
Kathryn E
KE
Seth-Smith
Helena M B
HM
Quail
Michael A
MA
Rance
Richard
R
Brooks
Karen
K
Churcher
Carol
C
Harris
David
D
Bentley
Stephen D
SD
Burrows
Christine
C
Clark
Louise
L
Corton
Craig
C
Murray
Vicky
V
Rose
Graham
G
Thurston
Scott
S
van Tonder
Andries
A
Walker
Danielle
D
Wren
Brendan W
BW
Dougan
Gordon
G
Parkhill
Julian
J
D016360:Clostridioides difficile / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D018014:Gene Transfer Techniques; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013997:Time Factors; D014774:Virulence