Background
Methods
Bacterial strains
Genome sequencing, assembly, and annotation
Sequence analysis and comparative genomics
Results
Phylogeny
Overview of the C. difficile ST201 genomes
Strain | LC693 | VL-0104 | VL-0391 | R20291 | M120 |
---|---|---|---|---|---|
Places of isolation | China | Canada | Canada | UK | UK |
Ribotype | – | – | – | 027 | 078 |
Sequence type | ST201 | ST201 | ST201 | ST1 | ST11 |
Toxin profile | A + B + CDT+ | A + B + CDT+ | A + B + CDT+ | A + B + CDT+ | A + B + CDT+ |
Genome completion | Draft | Draft | Draft | Complete | Complete |
Genome size (bp) | 4,073,021 | 4,068,388 | 4,160,703 | 4,191,339 | 4,047,729 |
GC% | 28.5 | 28.7 | 28.9 | 28.6 | 28.7 |
Predicted CDSs | 3868 | 3833 | 3832 | 3508 | 3490 |
Predicted tRNAs | 79 | 77 | 69 | 65 | 86 |
Predicted rRNAs | 9 | 11 | 41 | 28 | 32 |
Plasmid | 0 | 0 | 0 | 0 | 0 |
Prophages | 7 (3a) | 7 (2a) | 8 (3a) | 4 (2a) | 4 (1a) |
Antibiotic resistance associated genes
Locus in LC693 | Locus in VL-0104 | Locus in VL-0391 | Length (aa) | Description | Resistance | Presence in R20291 | Presence in M120 |
---|---|---|---|---|---|---|---|
0042 | 2926 | 1001 | 196 | Virginiamycin A acetyltransferase, which can inactivate the target drug | Streptogramin_a | + | + |
0115 | 2999 | 1075 | 197 | Virginiamycin A acetyltransferase, which can inactivate the target drug | Streptogramin_a | + | − |
0120 | 3004 | 1080 | 241 | VanA type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-lactate | Teicoplanin; vancomycin | + | + |
0267 | 3195 | 1228 | 65 | Major facilitator superfamily transporter. Multidrug resistance efflux pump | Deoxycholate; fosfomycin | − | + |
0402 | 3309 | 1347 | 228 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
0410 | 3317 | 1355 | 228 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
0412 | 3319 | 1357 | 223 | VanA type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-lactate | Teicoplanin; vancomycin | + | + |
0416 | 3323 | 1361 | 221 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide1094 | + | + |
0576 | 3486 | 1519 | 222 | VanB type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-lactate | Vancomycin | + | + |
0580 | 3490 | 1523 | 607 | Ribosomal protection protein, which protects ribosome from the translation inhibition of tetracycline | Tetracycline | + | + |
0601 | 3511 | 1544 | 67 | VanG type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-serine | Vancomycin | + | + |
0699 | 3617 | 1658 | 210 | Virginiamycin A acetyltransferase, which can inactivate the target drug | Streptogramin_a | + | + |
0805 | 3681 | 1722 | 230 | VanG type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-serine | Vancomycin | + | + |
0820 | 3697 | 1738 | 238 | VanG type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-serine | Vancomycin | + | + |
1054 | 0094 | 1967 | 227 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
1094 | 0134 | 2007 | 238 | VanG type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-serine | Vancomycin | + | + |
1247 | 0352 | 2230 | 234 | VanA type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-lactate | Teicoplanin; vancomycin | + | + |
1500 | 0582 | 2467 | 283 | Undecaprenyl pyrophosphate phosphatase, which consists in the sequestration of Undecaprenyl pyrophosphate | Bacitracin | + | + |
1568 | 0651 | 2535 | 250 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
1685 | 0767 | − | 238 | VanG type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-serine | Vancomycin | − | − |
1799 | 0854 | 2700 | 110 | ABC transporter system, bacitracin efflux pump | Bacitracin | − | − |
1869 | 0925 | 3336 | 371 | VanA type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-lactate | Teicoplanin; vancomycin | + | − |
1870 | 0926 | 3337 | 232 | VanA type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-lactate | Teicoplanin; vancomycin | + | − |
1962 | 1044 | 2900 | 276 | VanG type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-serine | Vancomycin | + | − |
2234 | 1252 | 3136 | 228 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
2251 | 1268 | 3166 | 230 | VanG type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-serine | Vancomycin | + | + |
2272 | 1289 | 3187 | 288 | Pentapeptide repeat family, which protects DNA gyrase from the inhibition of quinolones | Fluoroquinolone | + | + |
2466 | 1548 | 3530 | 305 | ABC transporter system, bacitracin efflux pump | Bacitracin | + | + |
2642 | 1673 | 3662 | 227 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
2655 | 1998 | 3676 | 234 | ABC transporter system, bacitracin efflux pump | Bacitracin | + | + |
2658 | 1995 | 3679 | 230 | VanA type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-lactate | Teicoplanin; vancomycin | + | + |
2661 | 1992 | 3682 | 222 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
2663 | 1990 | 3684 | 224 | VanE type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine-d-serine | Vancomycin | + | + |
2831 | 1853 | 0043 | 304 | ABC transporter system, bacitracin efflux pump | Bacitracin | + | + |
2922 | 2024 | 0104 | 192 | Virginiamycin A acetyltransferase, which can inactivate the target drug | Streptogramin_a | − | + |
3194 | 2245 | 0335 | 227 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
3599 | 2639 | 0706 | 274 | Undecaprenyl pyrophosphate phosphatase, which consists in the sequestration of Undecaprenyl pyrophosphate | Bacitracin | + | + |
3614 | 2654 | 0729 | 235 | ABC transporter system, bacitracin efflux pump | Bacitracin | + | + |
3781 | 2789 | 0865 | 225 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
3846 | 2855 | 0930 | 224 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | + | + |
− | − | 1192 | 71 | Resistance-nodulation-cell division transporter system. Multidrug resistance efflux pump. Macrolide-specific efflux system | Macrolide | − | − |
− | − | 3284 | 174 | VanG type vancomycin resistance operon genes, which can synthesize peptidoglycan with modified C-terminal d-Ala-d-Ala to d-alanine–d-serine | Vancomycin | − | − |
Prophage identification
Phage region | Region length (kb) | Completeness | #CDS | Possible phage | GC (%) |
---|---|---|---|---|---|
Strain LC693 | |||||
1 | 28.3 | Incomplete | 24 | PHAGE_Clostr_phiCD505_NC_028764 (6) | 27.38 |
2 | 19.7 | Incomplete | 47 | PHAGE_Clostr_CDMH1_NC_024144 (21) | 28.15 |
3 | 71.7 | Intact | 102 | PHAGE_Clostr_phiCDHM19_NC_028996 (35) | 29.33 |
4 | 27.1 | Incomplete | 31 | PHAGE_Clostr_phiCDHM19_NC_028996 (11) | 28.04 |
5 | 7.4 | Questionable | 6 | PHAGE_Paenib_Xenia_NC_028837 (2) | 30.32 |
6 | 67.2 | Intact | 88 | PHAGE_Clostr_phiMMP02_NC_019421 (30) | 28.69 |
7 | 24.1 | Intact | 45 | PHAGE_Clostr_c_st_NC_007581 (6) | 33.26 |
Strain VL-0104 | |||||
1 | 22.4 | Incomplete | 19 | PHAGE_Clostr_c_st_NC_007581 (3) | 28.77 |
2 | 48.3 | Intact | 58 | PHAGE_Clostr_CDMH1_NC_024144 (22) | 28.44 |
3 | 27.1 | Incomplete | 31 | PHAGE_Clostr_phiCDHM19_NC_028996 (11) | 28.04 |
4 | 48.4 | Intact | 69 | PHAGE_Clostr_phiCD505_NC_028764 (24) | 28.27 |
5 | 7.4 | Questionable | 6 | PHAGE_Paenib_Xenia_NC_028837 (2) | 30.32 |
6 | 15.6 | Incomplete | 27 | PHAGE_Clostr_phiCD27_NC_011398 (14) | 29.98 |
7 | 11.2 | Questionable | 18 | PHAGE_Clostr_c_st_NC_007581 (4) | 31.68 |
Strain VL-0391 | |||||
1 | 22.6 | Incomplete | 18 | PHAGE_Clostr_c_st_NC_007581 (3) | 28.79 |
2 | 33.3 | Intact | 39 | PHAGE_Clostr_phiMMP03_NC_028959 (8) | 27.45 |
3 | 27.1 | Incomplete | 31 | PHAGE_Clostr_phiCDHM19_NC_028996 (11) | 28.04 |
4 | 51.4 | Intact | 69 | PHAGE_Clostr_phiCD505_NC_028764 (23) | 28.06 |
5 | 7.4 | Questionable | 6 | PHAGE_Paenib_Xenia_NC_028837 (2) | 30.32 |
6 | 34.9 | Questionable | 37 | PHAGE_Clostr_CDMH1_NC_024144 (15) | 31.25 |
7 | 25.3 | Incomplete | 34 | PHAGE_Clostr_phiCD27_NC_011398 (12) | 31.52 |
8 | 11.1 | Intact | 23 | PHAGE_Clostr_c_st_NC_007581 (3) | 32.47 |
Single nucleotide polymorphisms
Nos. of SNPs | Non-synonymous | Synonymous | DN/dS | |
---|---|---|---|---|
LC693 vs. R20291 | 54,837 (41,696a) | 15,172 | 26,524 | 0.57 |
VL-0104 vs. R20291 | 52,580 (39,912a) | 14,687 | 25,225 | 0.58 |
VL-0319 vs. R20291 | 52,447 (39,065a) | 14,127 | 24,938 | 0.57 |
Subtotal | 159,864 (120,673a) | 43,986 | 76,687 | 0.57 |
LC693 vs. M120 | 107,738 (82,855a) | 25,643 | 57,212 | 0.45 |
VL-0104 vs. M120 | 107,889 (82,872a) | 26,258 | 56,614 | 0.46 |
VL-0319 vs. M120 | 107,694 (81,424a) | 25,046 | 56,378 | 0.44 |
Subtotal | 323,321 (247,151a) | 76,947 | 170,204 | 0.45 |
Sequence analysis of PaLoc
Strains |
tcdR
|
tcdB
|
tcdE
| Tn6218
|
tcdA
|
tcdC
| ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
tnt
|
xis
|
rep
|
xre
|
merR
| Oxidoreductase | Flavodoxin | orf | σ70 | ||||||
Against R20291 (ST1/027, clade 2) | ||||||||||||||
LC693 | 13 | 459 | 3 (72 del) | – | – | – | – | – | – | – | – | – | 100 | 5 (144 del) |
VL-0104 | 13 | 459 | 3 (72 del) | – | – | – | – | – | – | – | – | – | 100 | 5 (144 del) |
VL-0391 | 13 | 459 | 3 (72 del) | – | – | – | – | – | – | – | – | – | 100 | 5 (144 del) |
Against M120 (ST11/078, clade 5) | ||||||||||||||
LC693 | 18 | 175 | 2 (72 del) | – | – | – | – | – | – | – | – | – | 90 | 3 (264 del + 20 in) |
VL-0104 | 18 | 175 | 2 (72 del) | – | – | – | – | – | – | – | – | – | 90 | 3 (264 del + 20 in) |
VL-0391 | 18 | 175 | 2 (72 del) | – | – | – | – | – | – | – | – | – | 90 | 3 (264 del + 20 in) |