Peptoclostridium difficile

Peptoclostridium difficile is a major nosocomial pathogen world-wide causing disease ranging from antibiotic-associated diarrhoea to life-threatening pseudomembranous colitis.

Data Downloads

• FTP site

• BLAST server

We have completed the genome sequencing of Peptoclostridium difficile strain 630. Strain 630 is multi-drug resistant, and was isolated from a patient with severe PMC that had spread to dozens of other patients on the same ward in Zurich, Switzerland in 1982. Thus strain 630 has the genetic attributes of a fully virulent, highly transmissible, drug resistant strain. This work was carried out in collaboration with Brendan Wren of the London School of Hygiene and Tropical Medicine, Neil Fairweather and Gordon Dougan of the Centre for Molecular Microbiology and Infection, Imperial College, London and Peter Mullany of the Eastman Dental Institute, London.

We have also sequenced several other strains of P. difficile, including P. difficile strain R20291 (SM), P. difficile strain 196, P. difficile strain BI1, P. difficile strain M120 and P. difficile strain M68.

Published Genome Data

Published Reference Genome

The Sanger Institute completed the sequencing of Peptoclostridium difficile strain 630 (epidemic type X) in 2006. The genome consists of a circular chromosome of 4,290,252 bp with a G+C content of 29.06%, and a circular plasmid of 7,881 bp with a G+C content of 27.9%. The fully annotated chromosome and plasmid are available from the EMBL/GenBank databases with accession numbers AM180355 and AM180356 respectively. Using a combined transcriptomic and proteomic approach the annotation of Peptoclostridium difficile strain 630 has been updated in 2014 and is available as an embl file. This embl file contains functional class and colour annotation characterising genes into broad functional groups that is not present on the updated EMBL/GenBank version. The embl file along with the key to the colour and class annotation is available from our FTP site. The original shotgun and assembly data can also still be accessed here. The embl file can be interrogated using Artemis which is available as a free download from the Related links on this page.

Other Published Genomes

The Sanger Institute has completed sequencing and assembly of several further strains of P. difficile as follows :

P. difficile strain 196

• Isolated: France, 1985 (Ribotype 027)
• Shotgun: 33,509 reads totalling 20.887 Mb, theoretical genome coverage of 99.26%
• Assembly/Annotation: FN538970

P. difficile strain BI1

• Isolated: USA, 1988 (Ribotype 027)
• Shotgun: 34,428 reads totalling 21.622 Mb, theoretical genome coverage of 99.33%
• Assembly/Annotation: FN668941, FN668942, FN668943

P. difficile strain M120

• Isolated: UK, 2007 (Ribotype 078)
• Shotgun: 32,381 reads totalling 21.754 Mb, theoretical genome coverage of 99.33%
• Assembly/Annotation: FN665653

P. difficile strain M68

• Isolated: Ireland, 2006 (Ribotype 017)
• Shotgun: 29,958 reads totalling 18.975 Mb, theoretical genome coverage of 98.77%
• Assembly/Annotation: FN668375

P. difficile strain SM (R20291)

• Isolated: UK, 2006 (Ribotype 027)
• Shotgun: 34,018 reads totalling 22.599 Mb, theoretical genome coverage of 99.45%
• Assembly/Annotation: FN545816

P. difficile strain CF5

• Isolated: Belgium, 1995 (Ribotype 017)
• Shotgun: 34,226 reads totalling 23.359 Mb, theoretical genome coverage of 99.99%
• Assembly/Annotation: FN665652

P. difficile strain 855

• Isolated: USA, 2007 (Ribotype 027)
• Shotgun: 33,918 reads totalling 22.907 Mb, theoretical genome coverage of 99.99%
• Assembly/Annotation: FN665654

Shotgun and assembly data from these projects are available from our ftp site.