Table 2.
General features of the 60 C. difficile genomes employed in this studya
| Strain name (accession no.) | Genome statusa (no. of contigs) |
Total sizea (Mb) |
No. of genesa | G + C contenta(%) | MLST cladeb | STsb | Sampling country |
|---|---|---|---|---|---|---|---|
| C. difficile CBA7201 (QKRF00000000)c | C (3) | 4.34 | 4,107 | 28.8 | 1 | 17 | Korea |
| C. difficile CBA7202 (QLNX00000000)c | D (3) | 4.40 | 4,204 | 28.8 | 1 | 17 | Korea |
| C. difficile CBA7203 (QKRE00000000)c | D (5) | 4.39 | 4,189 | 28.8 | 1 | 17 | Korea |
| C. difficile CBA7204 (CP029566)c | C (1) | 4.04 | 3,744 | 28.5 | 1 | 203 | Korea |
| C. difficile CBA7205 (QLNY00000000)c | D (7) | 4.40 | 4,176 | 28.9 | 1 | 17 | Korea |
| C. difficile CBA7206 (QLNZ00000000)c | D (7) | 4.16 | 3,911 | 28.7 | 1 | 8 | Korea |
| C. difficile CBA7207 (QLOA00000000)c | D (2) | 4.33 | 4,101 | 28.8 | 1 | 17 | Korea |
| C. difficile CBA7208 (QKRD00000000)c | C (2) | 4.08 | 3,786 | 28.5 | 1 | 4 | Korea |
| C. difficile CBA7209 (QLOB00000000)c | D (2) | 4.40 | 4,191 | 28.8 | 1 | 17 | Korea |
|
C. difficile 630 (AM180355-6) C. difficile DSM 27639 (CP011847) C. difficile DSM 29745 (CP019857) C. difficile DSM 29688 (CP019858) C. difficile W0022a (CP025046) C. difficile DSM 29632 (CP019860) C. difficile 08ACD0030 (CP010888) C. difficile BR81 (CP019870) C. difficile Mta-79 (CP042267) C. difficile DSM 28666 (CP012321) C. difficile DSM 29637 (CP016106) C. difficile W0023a (CP025045) C. difficile FDAARGOS_267 (CP020424-6) C. difficile DH/NAP11/106/ST-42 (CP022524) C. difficile W0003a (CP025047) C. difficile 020477 (CP028524) C. difficile 020709 (CP028529) C. difficile QCD-63q42 (CM000637) C. difficile DSM 1296 T (CP011968-9) C. difficile DSM 27638 (CP011846) C. difficile DSM 27640 (CP011848) C. difficile CD-17-01474 (CP026591) C. difficile R0104a (CP025044) C. difficile 08-00495 (CP026594) C. difficile 10-00253 (CP026598) C. difficile 12-00011 (CP026595) C. difficile 09-00072 (CP026599) C. difficile 10-00,078 (CP026597) C. difficile 10-00071 (CP026596) C. difficile 12-00008 (CP026593) C. difficile CD-10-00484 (CP026592) C. difficile CD196 (FN538970) C. difficile QCD-66c26 (CM000441) C. difficile DSM 102860 (CP020379) C. difficile DSM 102859 (CP020378) C. difficile VL_0104 (FAAJ00000000) C. difficile VL_0391 (FALK00000000) C. difficile ZJCDC-S82 (JYNK00000000) C. difficile CDT4 (CP029152-3) C. difficile DSM 29627 (CP016102) C. difficile DSM 28670 (CP012312) C. difficile CD161 (CP029154-6) C. difficile DSM 28669 (CP012323) C. difficile DSM 29629 (CP016104) C. difficile M68 (FN668375) C. difficile DSM 29747 (CP019864) C. difficile 12038 (CP033214-5) C. difficile CD10010 (CP033213) C. difficile M120 (FN665653) C. difficile CD21062 (CP033216-7) C. difficile DSM 29,020 (CP012325) |
C (2) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (3) C (1) C (1) C (1) C (1) D (28) C (2) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) C (1) D (15) C (1) C (1) D (261) D (1,092) D (20) C (2) C (1) C (1) C (3) C (1) C (1) C (1) C (1) C (2) C (1) C (1) C (2) C (1) |
4.29 4.26 4.24 4.22 4.18 4.17 4.16 4.12 4.12 4.12 4.11 4.11 4.28 4.08 4.07 4.14 4.09 4.44 4.28 4.22 4.22 4.20 4.19 4.17 4.12 4.11 4.11 4.11 4.11 4.11 4.11 4.11 4.12 4.25 4.24 4.06 4.16 4.22 4.28 4.20 4.19 4.47 4.13 4.11 4.3 4.07 4.07 4.04 4.04 4.10 4.13 |
3981 4026 3975 4041 3942 3891 3907 3813 3844 3829 3844 3804 4049 3743 3765 3873 3792 4213 3984 3966 3964 3939 3924 3902 3,844 3,845 3,842 3,845 3843 3842 3843 3807 3774 4071 4050 3,859 3939 3934 4035 3916 3962 4277 3908 3802 4025 3809 3822 3785 3756 3898 3905 |
29.0 29.1 29.0 28.9 28.9 28.6 28.8 28.7 28.7 29.0 28.6 28.7 28.7 28.6 28.6 28.8 28.5 28.6 28.7 29.0 29.0 28.9 28.7 28.7 28.6 28.6 28.6 28.6 28.6 28.6 28.6 28.6 28.5 29.0 29.0 28.7 29.0 29.1 28.8 28.8 28.8 28.8 28.8 28.6 28.9 29.1 28.8 28.7 28.7 28.9 29.2 |
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 4 4 4 4 4 4 4 5 5 5 5 5 5 |
54 54 3 15 2 103 2 42 34 48 83 42 3 42 8 110 21 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 5 201 201 5 37 37 38 37 109 39 37 11 11 11 11 11 11 |
Switzerland Germany Germany Germany USA Indonesia Canada Korea USA Ghana Indonesia USA USA USA USA USA USA Canada UK Germany Germany Germany USA Germany Germany Germany Germany Germany Germany Germany Germany France Canada Germany Germany Canada Canada China China Indonesia Ghana China Ghana Indonesia Ireland Germany China China UK China Indonesia |
aBioinformatic genome analysis was carried out using the NCBI prokaryotic genome annotation pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/)
bMLST clade and ST information was obtained using PubMLST analysis (https://pubmlst.org/cdifficile/)
cGenomes sequenced in this study are highlighted in bold
dGenome status: D draft genome sequence, C complete genome sequence