William Hanage's Faculty Website

MLST

MLST for Streptococcus pneumoniae

Multi-Locus Sequence Typing (MLST) was developed as a portable, unambiguous method for molecular epidemiology of bacterial pathogens. It defines ‘Sequence Types’ or STs on the basis of variation at multiple (usually seven) pre-defined loci throughout the genome. Two isolates identical at all sites are certainly closely related.

Illustration of MLST. Loci are amplified by PCR, sequenced, and each unique allele assigned an allele number, and each unique combination of alleles determines the Sequence Type. The illustration reflects Sanger Sequencing, but we now accept results from Next-Gen methods.
Illustration of MLST. Loci are amplified by PCR, sequenced, and each unique allele assigned an allele number, and each unique combination of alleles determines the Sequence Type. The illustration reflects Sanger Sequencing, but we now accept results from Next-Gen methods.

Because each unique allele is defined as an integer (the ‘allele number’) and comparisons are based on the numbers of alleles isolates have in common, the method resists being distorted by recombination: if isolates differ at a single allele which harbors many SNPs, they were almost certainly introduced by recombination, and so should be considered as one event.

Part of a comparative eBURST diagram constructed from MLST data. For figure see Chang et al 2015
Part of a comparative eBURST diagram constructed from MLST data. For figure see Chang et al 2015

Dr Hanage is one of the three curators of the MLST database for Streptococcus pneumoniae, hosted by the University of Oxford in the UK. Details of how to submit data, obtain allele numbers and sequence types, can be found here. Please note that the previous database at http://spneumoniae.mlst.net has now been migrated to the above link, and is now longer up to date.