Evolutionary dynamics of Clostridium difficile over short and long time scales

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7527-32. doi: 10.1073/pnas.0914322107. Epub 2010 Apr 5.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clostridioides difficile / genetics*
  • Computational Biology
  • Evolution, Molecular*
  • Gene Expression Regulation, Bacterial
  • Gene Transfer Techniques
  • Genome, Bacterial
  • Molecular Sequence Data
  • Phylogeny
  • Polymerase Chain Reaction
  • Polymorphism, Single Nucleotide
  • Recombination, Genetic
  • Sequence Analysis, DNA
  • Species Specificity
  • Time Factors
  • Virulence

Associated data

  • GENBANK/FN545816
  • GENBANK/FN665652
  • GENBANK/FN665653
  • GENBANK/FN668375
  • GENBANK/FN668941
  • GENBANK/FN668942
  • GENBANK/FN668943
  • GENBANK/FN668944