Variable Number Tandem Repeat Typing of Bacteria

Analysis of bacterial genomes revealed a high percentage of DNA consisting of repeats, in which DNA motifs existed in multiple copies. Study of these DNA motifs has resulted in the development of variable number tandem repeat (VNTR) or multilocus variant-repeat analysis (MLVA) assays, which have shown to be valuable bacterial typing methods, especially in relation to disease outbreaks. The VNTR-based assay is based on direct PCR amplification of a specific locus, which is well defined. The range and polymorphism index of each locus can be calculated. This chapter describes the VNTR analysis of Neisseria meningitides -based on separation in low resolution media agarose, and VNTR analysis of Salmonella enterica subsp. enterica serovars Typhimurium-based on high resolution capillary electrophoresis.