Open AccessSingle Nucleotide Polymorphism Typing of Global Salmonella enterica Serovar Typhi Isolates by Use of a Hairpin Primer Real-Time PCR Assay
Author(s) -
Sophie Octavia,
Ruiting Lan
Publication year - 2010
Publication title -
journal of clinical microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.349
H-Index - 255
eISSN - 1070-633X
pISSN - 0095-1137
DOI - 10.1128/jcm.00709-10
Subject(s) - salmonella enterica , biology , serotype , single nucleotide polymorphism , typing , salmonella typhi , primer (cosmetics) , genetics , snp , polymerase chain reaction , microbiology and biotechnology , virology , salmonella , genotype , gene , bacteria , escherichia coli , chemistry , organic chemistry
Salmonella enterica serovar Typhi is highly homogeneous. Single nucleotide polymorphisms (SNPs) have been shown to be valuable markers for molecular typing ofS. enterica serovar Typhi. Here, we used a hairpin primer real-time PCR assay for SNP typing ofS. enterica serovar Typhi isolates. Forty-two SNPs were selected from a comparison of 19 publishedS. enterica serovar Typhi genomes and sequences from other studies. The SNPs were used to type 71 globalS. enterica serovar Typhi isolates and differentiated theseS. 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.