@article{mbs:/content/journal/jmm/10.1099/jmm.0.05365-0, author = "Robertson, Gail A. and Thiruvenkataswamy, Venugopal and Shilling, Hayden and Price, Erin P. and Huygens, Flavia and Henskens, Frans A. and Giffard, Philip M.", title = "Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases", journal= "Journal of Medical Microbiology", year = "2004", volume = "53", number = "1", pages = "35-45", doi = "https://doi.org/10.1099/jmm.0.05365-0", url = "https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.05365-0", publisher = "Microbiology Society", issn = "1473-5644", type = "Journal Article", 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 (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.", }