1887

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 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 (), and may thus be generally applicable to that species. SNP sets that are diagnostic for ST-11 and ST-42, and high- SNP sets for and , were identified and real-time PCR methods to interrogate these SNPs were demonstrated. High- SNP sets were also identified in other MLST databases. This widely applicable approach allows rapid genetic fingerprinting of infectious agents.

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2004-01-01
2020-07-08
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