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

G A Robertson; V Thiruvenkataswamy; H Shilling; Erin P Price; F Huygens; F A Henskens; P M Giffard

doi:10.1099/jmm.0.05365-0

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

Journal article

Peer reviewed

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

G A Robertson, V Thiruvenkataswamy, H Shilling, Erin P Price, F Huygens, F A Henskens and P M Giffard

Journal of Medical Microbiology, Vol.53(1), pp.35-45

2004

DOI: https://doi.org/10.1099/jmm.0.05365-0

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Abstract

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 seq uence 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.

Details

Title: Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases
Authors: G A Robertson (Author) - Queensland University of Technology
V Thiruvenkataswamy (Author) - Queensland University of Technology
H Shilling (Author) - Queensland University of Technology
Erin P Price (Author) - Queensland University of Technology
F Huygens (Author) - Queensland University of Technology
F A Henskens (Author) - University of Newcastle
P M Giffard (Author) - Queensland University of Technology
Publication details: Journal of Medical Microbiology, Vol.53(1), pp.35-45
Publisher: Microbiology Society
Date published: 2004
DOI: 10.1099/jmm.0.05365-0
ISSN: 0022-2615
Organisation Unit: University of the Sunshine Coast, Queensland; Centre for Bioinnovation
Language: English
Record Identifier: 99451050202621
Output Type: Journal article

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