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)