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)