Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases

J Med Microbiol. 2004 Jan;53(Pt 1):35-45. doi: 10.1099/jmm.0.05365-0.


A unified, bioinformatics-driven, single nucleotide polymorphism (SNP)-based approach to microbial genotyping has been developed. Multilocus sequence typing (MLST) databases consist of known variants of standardized housekeeping genes. Normally, seven fragments are defined; a sequence type (ST) consists of the variants of these fragments that are found in a particular isolate. A computer program that can identify highly informative sets of SNPs in entire MLST databases has been constructed. The SNPs either define a particular user-specified ST or provide a high value for Simpson's index of diversity (D), and may thus be generally applicable to that species. SNP sets that are diagnostic for Neisseria meningitidis ST-11 and ST-42, and high-D SNP sets for N. meningitidis and Staphylococcus aureus, were identified and real-time PCR methods to interrogate these SNPs were demonstrated. High-D SNP sets were also identified in other MLST databases. This widely applicable approach allows rapid genetic fingerprinting of infectious agents.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Bacterial Typing Techniques / methods*
  • DNA Primers / chemistry
  • DNA, Bacterial / chemistry
  • Databases, Nucleic Acid*
  • Genetic Variation
  • Genotype
  • Humans
  • Kinetics
  • Neisseria meningitidis / classification*
  • Neisseria meningitidis / genetics
  • Polymerase Chain Reaction / methods
  • Polymorphism, Single Nucleotide*
  • Sequence Alignment
  • Software
  • Staphylococcus aureus / classification*
  • Staphylococcus aureus / genetics


  • DNA Primers
  • DNA, Bacterial