MLST Revisited: The Gene-By-Gene Approach to Bacterial Genomics

Nat Rev Microbiol. 2013 Oct;11(10):728-36. doi: 10.1038/nrmicro3093. Epub 2013 Sep 2.

Abstract

Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Alleles
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacterial Typing Techniques / methods
  • Base Sequence
  • Databases, Genetic
  • Evolution, Molecular
  • Genetic Variation
  • Genome, Bacterial*
  • Genomics / methods*
  • Multilocus Sequence Typing / methods*
  • RNA, Bacterial / analysis
  • RNA, Bacterial / genetics
  • RNA, Ribosomal, 16S / analysis
  • RNA, Ribosomal, 16S / genetics

Substances

  • RNA, Bacterial
  • RNA, Ribosomal, 16S