- Title
- Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases
- Creator
- Robertson, Gail A.; Thiruvenkataswamy, Venugopal; Shilling, Hayden; Price, Erin P.; Huygens, Flavia; Henskens, Frans A.; Giffard, Philip M.
- Relation
- Journal of Medical Microbiology Vol. 53, Issue 1, p. 35-45
- Publisher Link
- http://dx.doi.org/10.1099/jmm.0.05365-0
- Publisher
- Society for General Microbiology
- Resource Type
- journal article
- Date
- 2004
- Description
- 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.
- Subject
- single nucleotide polymorphism; sequence type; Simpson's index of diversity; multilocus sequence typing; MLST; SNP; methicillin-resistant Staphylococcus aureus; MRSA
- Identifier
- uon:1796
- Identifier
- http://hdl.handle.net/1959.13/27562
- Identifier
- ISSN:0022-2615
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