Details of assembly methods and in silico genotyping for Escherichia

  • 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 2,513 Loci 25,002 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

Classic MLST scheme is described in Wirth et al (2006) Mol. Microbiol. 60(5), 1136-1151.

Genes included in 7 gene MLST (together with the length of sequence used for MLST taken from figure 1 in the above cited paper):

Gene Length
adk 536
fumC 469
gyrB 460
icd 518
mdh 452
recA 510
purA 478

Ribosomal MLST (rMLST)