Extrachromosomal and integrated genetic elements in Clostridium difficile.

•Clostridium difficile causes gastrointestinal disease in antibiotic-treated patients.•Clostridium difficile contains many extrachromosomal and integrated genetic elements.•Recent genomic work has given new insights into the variability and distribution of Clostridium difficile elements.•Thirty years of research and the function of mobile genetic elements in Clostridium difficile phenotypes is discussed.•We review Clostridium difficile antibiotic resistance determinants associated with mobile genetic elements.