Sequence analysis of the variable number tandem repeat in Staphylococcus aureus protein A gene: spa typing

The analyses of numerous prokaryotic and eukaryotic genomes have revealed the presence of variable number tandem repeats (VNTRs). VNTR analysis is currently widely used to sub-speciate many bacterial, fungal, and viral pathogens and has facilitated a number of molecular epidemiology studies. In this chapter, we focus on spa typing which is based on sequence analysis of VNTRs in the polymorphic X region of the Staphylococcus aureus protein A gene Staphylococcus aureus. As the specific methods for spa typing, detailed in this chapter, are well-established and routine procedures (e.g., DNA isolation, PCR and DNA sequencing) for most molecular biology laboratories, we highlight the analytic methods used to interpret the genotyping data generated by sequence analysis and their potential applications in local and global epidemiologic investigations.