Details of assembly methods and in silico genotyping for Clostridioides¶
- All MLST-like typing methods in EnteroBase are derived from a genome assembly of sequenced reads. For an explanation of this method, see here
- For a general description of the in silico typing method, see here
| MLST – Classic | Ribosomal MLST (Jolley, 2012) | Core Genome MLST | Whole Genome MLST |
|---|---|---|---|
| 7 Loci | 53 Loci | 2,556 Loci | 11,490 Loci |
| Conserved Housekeeping genes | Ribosomal proteins | Core genes | Any coding sequence |
| Highly conserved; Low resolution | Highly conserved; Medium resolution | Variable; High resolution | Highly variable; Extreme resolution |
| Different scheme for each species/genus | Single scheme across tree of life | Different scheme for each species/genus | Different scheme for each species/genus |
7 Gene MLST¶
The classic MLST scheme for Clostridioides is described in Griffiths et al (2010) J. Clin. Microbiol. 48, 770-778.
Genes included in 7 gene MLST (together with the length of sequence used for MLST taken from table 1 in the above cited paper):
| Gene | Length |
|---|---|
| adk | 501 |
| atpA | 555 |
| dxr | 411 |
| glyA | 516 |
| recA | 564 |
| sodA | 450 |
| tpi | 504 |
Ribosomal MLST (rMLST)¶
- rMLST is Copyright © 2010-2016, University of Oxford. rMLST is described in Jolley et al. 2012 Microbiology 158:1005-15.