Multiple-locus variable-number tandem-repeat analysis of Salmonella enterica serovar Typhi

Abstract

Multilocus variable-number tandem repeats (VNTRs) are widely used as molecular markers to differentiate isolates of homogenous pathogenic clones. We explored the genomes of Salmonella enterica serovar Typhi strains CT18 and Ty2 for potential VNTRs. Among the 43 potential VNTRs screened, 2 were found to be polymorphic. Together with seven polymorphic VNTRs from previous studies, they were used to type 73 global serovar Typhi isolates. A total of 70 multilocus VNTR analysis (MLVA) profiles were found, distinguishing all except three pairs of isolates into individual profiles. The discriminatory power was 0.999. Phylogenetic analysis showed that the MLVA profiles can be divided into seven clusters. However, except for the closely related isolates, the relationships derived were in conflict with those inferred from single nucleotide polymorphism (SNP) typing using 38 SNPs done previously. We concluded that MLVA can resolve the relationships only among closely related isolates. A combination of SNP typing and MLVA typing offers the best approach for local and global epidemiology and the evolutionary analysis of serovar Typhi. We suggest that seven of the nine most polymorphic VNTRs be used as a standardized typing scheme for epidemiological typing.

FIG. 1.

UPGMA dendrogram of the 70 MLVA profiles. The assigned clusters are indicated by roman numerals. Bootstrap values, if greater than 50%, are presented at the nodes of the tree. The table to the right of the dendrogram shows the allelic pattern for each MLVA profile. The shaded numbers are the alleles that supported the clustering of the MLVA profiles.

FIG. 2.

A composite tree combining an MST tree generated using SNP and an MST using VNTR data. A secondary MST was generated only for SNP profiles containing more than two MLVA profiles, and the MST for the corresponding SNP profile is located adjacent to the given SNP profile. The numbers on the MLVA MST trees indicate the number of differences in VNTR loci. The SNP clusters are indicated by roman numerals at the nodes. Members of SNP cluster II were omitted for clarity, as there was no further MLVA MST for any of the SNP profiles in this cluster. The scale bar represents five differences in VNTR loci.