MLST – MultiLocus Sequence Typing
Not a shiny new procedure, MLST has been around since 1998 .
MLST allows for the unambiguous characterization of isolates from infectious agents (predominantly bacteria, some fungi) using sequences of internal fragments of (usually) seven housekeeping genes. Gene regions of approximately 450–500 bp are sequenced and those found unique within a species are assigned an allele number. Each isolate is then characterized by the alleles at each of the seven loci, which constitute its allelic profile or sequence type (ST).
Each isolate of a species is therefore unambiguously characterised by a series of seven integers which correspond to the alleles at the seven house-keeping loci.
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 erroneously consider the allele to be more different than by treating the nucleotide changes as a single genetic event.
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 genotypes to be resolved.
The allelic profiles of isolates are then compared to existing databases.
- MLST allows accurate assessment of species, and sometimes down to strain level.
- Selection of housekeeping loci necessitates a reference genome.
- You need a MLST database
 Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. Multilocus sequence typing: a portable approach to the identification of clones within populations of
pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3140-5.
 Pérez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA. Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect Genet Evol. 2013 Jun;16:38-53.
- PuMLST has a comprehensive list of databases and appears to be updated regularly.
- The ever helpful tseemann has a nice MLST tool, handily called mlst.
- Web tool at the CGE Server.
- Links from this page: https://bacpathgenomics.wordpress.com/2012/08/25/mlst-from-short-read-data/