MLST in Microbial Molecular Identification

The analysis of nucleotide sequence data can be used to improve our understanding of bacterial species, genera, and populations. The main advantage of multilocus sequence typing (MLST) over other types of techniques is the non-fuzziness and transferability of sequence data. This technique not only meets the practical requirements of highly portable bacterial identification criteria but also is firmly rooted in the principles of population biology of multisite enzyme electrophoresis (MLEE). At Creative Biolabs, we have very experienced microbiologists who can provide microbial identification based on MLST technology

About MLST

MLST is a nucleotide sequence-based method to explicitly characterize bacterial species or strains of other microbial species via the Internet. MLST involves obtaining sequences of internal segments of seven housekeeping genes for each strain of a particular species. The sequence of each fragment is compared with all previously identified sequences (alleles) at that locus to assign an allele number to each of the seven loci. The combination of seven alleles defines the allele profile of the strain, and each different allele profile is designated as a sequence type (ST) that describes the strain.

The different levels of resolution afforded by alternative genetic markers.Fig.1 The different levels of resolution afforded by alternative genetic markers. (Cooper, 2004)

MLST Workflow

1. Each MLST species site provides users with many analytical steps. First, alleles must be assigned from sequence data in one of three ways:

  • Single/batch locus query
  • Multiple locus query
  • Batch strain query

2. If the user's sequence is found, the allele number is returned, and if the user has a new sequence, the percentage identifier of the closest allele in the database is returned.

3. This process was repeated for each locus to provide a 7-digit allelic of the queried strain. You can then enter a 7-digit allelic profile to find out if the strain in the allele profile is the same or similar to any strains that already exist in the database.

Graphical presentation of MLST data.Fig.2 Graphical presentation of MLST data. (Jolley, 2014)

Advantages of MLST

The use of MLST is a standard method for typing bacterial pathogens which have already provided a possible solution. Although MLST only typically examines seven core loci, which is a small sample, approx 0.1%, of the core genome of a species, clonal assignments inferred by MLST data are confirmed by analysis of complete genome sequences. The sequence data obtained from MLST can then be analyzed using numerous packages available on many websites.

Applications of MLST

MLST is now used for the characterization of a large number of organisms, including Streptococcus pneumoniae, Staphylococcus aureus, Campylobacter jejuni, Streptococcus pyogenes, and Haemophilus influenzae, as well as fungal species such as Candida albicans. This is not an exhaustive list of all existing MLST programs, excluding those under development.

The value of MLST lies in the provision of a comprehensive population framework based on multiple slowly evolving housekeeping loci. For species that contain sufficient diversity, this approach has proved valuable, both for routine typing and for evolutionary analysis. With our complete suite of microbial genomics solutions, Creative Biolabs can be your one-stop shop. Please contact us to discuss your next microbial identification project.


  1. Cooper, J.E.; Feil, E.J. Multilocus sequence typing-what is resolved? Trends in microbiology. 2004, 12(8): 373-377.
  2. Jolley, K.A.; Maiden, M.C.J. Using MLST to study bacterial variation: prospects in the genomic era. Future microbiology. 2014, 9(5): 623-630.

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