Single nucleotide polymorphism typing of global Salmonella enterica serovar Typhi isolates by use of a hairpin primer real-time PCR assay.

Salmonella enterica serovar Typhi is highly homogeneous. Single nucleotide polymorphisms (SNPs) have been shown to be valuable markers for molecular typing of S. enterica serovar Typhi. Here, we used a hairpin primer real-time PCR assay for SNP typing of S. enterica serovar Typhi isolates. Forty-two SNPs were selected from a comparison of 19 published S. enterica serovar Typhi genomes and sequences from other studies. The SNPs were used to type 71 global S. enterica serovar Typhi isolates and differentiated these S. enterica serovar Typhi isolates and the 19 genome sequenced strains into 25 SNP profiles. Phylogenetic analysis revealed that these SNP profiles were grouped into six major clusters. These clusters can be identified by using five SNPs, while the full differentiation of the 25 SNP profiles requires a minimum of 24 SNPs. This real-time PCR-based SNP typing method will be useful for global epidemiological analysis.