Table 1 Summary of protein clustering results within the different sub-clades containing the five toxin negative isolates included in this study. Summary of protein clusters within the different sub-clades of C. difficile

Genome names

No of predicted proteins

 Core genome

3323

  C. difficile C0000509

45

  C. difficile C0000541

38

  C. difficile C0000562

176

  C. difficile C00005945

212

  C. difficile H3

111

 Core genome

3357

  C. difficile 19.3

8

  C. difficile 22.1

7

  C. difficile C00000089

33

  C. difficile C000011286

86

  C. difficile C00006473

84

  C. difficile C00007671

35

  C. difficile C00011267

60

  C. difficile CF5

30

  C. difficile M68

19

  C. difficile P29

299