Multilocus sequence typing (MLST) is an unambiguous procedure for characterising isolates of bacterial (and other microbial) species using the sequences of internal fragments of multiple (typically seven) house-keeping genes*.
Approximately 450-500 bp internal fragments of each gene are used, as these can be accurately sequenced on both strands using an automated DNA sequencer.
For each house-keeping gene, the different sequences present among isolates of a bacterial species are assigned distinct allele numbers and, for each isolate, the alleles at each of the seven loci define its allelic profile (a series of seven integers).
To provide a simple strain nomenclature, each different allelic profile is assigned a different sequence type (ST) number (e.g. ST22).
*Multilocus typing schemes that mix house-keeping genes with other classes of gene (e.g. rRNA genes or genes under immune selection) should not be called MLST. The term MLST is restricted to schemes that only use (seven or more) house-keeping genes.
In MLST the number of nucleotide differences between alleles is ignored and sequences are given different allele numbers whether they differ at a single nucleotide site or at many sites. The rationale is that a single genetic event resulting in a new allele can occur by a point mutation (altering only a single nucleotide site), or by a recombinational replacement (that will often change multiple sites) - weighting according to the number of nucleotide differences between alleles would imply that the latter allele was more distantly-related to the original allele than the former, which would be true if all nucleotide changes occurred by mutation, but not if the changes occurred by a recombinational replacement.
Most bacterial species have sufficient variation within house-keeping genes to provide many alleles per locus, allowing billions of distinct allelic profiles to be distinguished using seven house-keeping loci. For example, an average of 30 alleles per locus allows about 20 billion multilocus genotypes to be resolved.
Bacterial and fungal species databases held at mlst.net
We host a number of MLST databases for the characterisation of isolates of bacterial or fungal species, containing allele sequences, STs and isolate information. Each database is accessible from its own website, which provides the same core functionality..
Facilities to query allele sequences, STs and epidemiological data that have been deposited in the database are provided. Furthermore, each MLST site contains tools to explore the population, including standard database querying, the clustering algorithm eBURST, tree drawing (using differences in either allelic profiles or concatenated allele sequences) and the ability to view and interrogate the data using Google Maps.
The menu on the front page of each species website provides basic information, such as who first described the scheme (and the reference), the primer sequences for PCR amplification of each house-keeping gene, contact details of the curator etc.
Instructions on how to use the websites are detailed in the next pages (use the menu on the left hand side of this page). Navigation of each site can be undertaken using the links at the top of each page.