Details of assembly methods and in silico genotyping for Yersinia

  • 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 Genom e MLST

7 Loci

51 Loci

1,553 Loci

19,53 1 Loci

Conserved Housekeeping genes

Ribosomal proteins

Core genes

Any codin g seque nce

Highly conserved; Low resolution

Highly conserved; Medium resolution

Variable; High resolution

Highl y varia ble; Extre me resol ution

Different scheme for each species/genus

Single scheme across tree of life

Different scheme for each species/genus

Diffe rent schem e for each speci es/ge nus

7 Gene MLST

Achtman 7 gene MLST scheme

The Achtman 7 gene MLST scheme is described in Laukkanen-Ninios et al (2011) Environ. Microbiol. 13(12), 3114-3127.

Genes included in Achtman 7 gene MLST (together with the length of sequence used for MLST taken from table 3 in the above cited paper):

Gene

Length

adk

389

argA

361

aroA

357

glnA

338

thrA

342

tmk

375

trpE

465

McNally 7 gene MLST scheme

The McNally 7 gene MLST scheme is described in Hall et al (2015) J. Clin. Microbiol. 53(1), 35-42.

Genes included in McNally 7 gene MLST (together with the length of sequence used for MLST taken from table 2 in the above cited paper):

Gene

Length

aarF

500

dfp

455

galR

500

glnS

442

hemA

490

speA

452

rfaE

429

Ribosomal MLST (rMLST)