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

51 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)