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.
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.
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.