Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases.
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.
Robertson
Gail A
GA
Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434 Brisbane, Queensland 4001, Australia 2Discipline of Computer Science and Software Engineering, University of Newcastle, Newcastle, New South Wales, Australia.
Thiruvenkataswamy
Venugopal
V
Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434 Brisbane, Queensland 4001, Australia 2Discipline of Computer Science and Software Engineering, University of Newcastle, Newcastle, New South Wales, Australia.
Shilling
Hayden
H
Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434 Brisbane, Queensland 4001, Australia 2Discipline of Computer Science and Software Engineering, University of Newcastle, Newcastle, New South Wales, Australia.
Price
Erin P
EP
Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434 Brisbane, Queensland 4001, Australia 2Discipline of Computer Science and Software Engineering, University of Newcastle, Newcastle, New South Wales, Australia.
Huygens
Flavia
F
Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434 Brisbane, Queensland 4001, Australia 2Discipline of Computer Science and Software Engineering, University of Newcastle, Newcastle, New South Wales, Australia.
Henskens
Frans A
FA
Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434 Brisbane, Queensland 4001, Australia 2Discipline of Computer Science and Software Engineering, University of Newcastle, Newcastle, New South Wales, Australia.
Giffard
Philip M
PM
Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434 Brisbane, Queensland 4001, Australia 2Discipline of Computer Science and Software Engineering, University of Newcastle, Newcastle, New South Wales, Australia.
D000465:Algorithms; D015373:Bacterial Typing Techniques / Q000379:methods*; D017931:DNA Primers / Q000737:chemistry; D004269:DNA, Bacterial / Q000737:chemistry; D030561:Databases, Nucleic Acid; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007700:Kinetics; D009345:Neisseria meningitidis / Q000145:classification* / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D012984:Software; D013211:Staphylococcus aureus / Q000145:classification* / Q000235:genetics
D017931:DNA Primers; D004269:DNA, Bacterial