Evolution of Variable Number Tandem Repeats and Its Relationship with Genomic Diversity in Salmonella Typhimurium.

Songzhe Fu,Mark M Tanaka,Qinning Wang,Sophie Octavia,Chin Yen Tay,Vitali Sintchenko,Ruiting Lan

doi:10.3389/fmicb.2016.02002

Abstract

Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing human infections in Australia and many other countries. A total of 12,112 S. Typhimurium isolates from New South Wales were analyzed by multi-locus variable number of tandem repeat (VNTR) analysis (MLVA) using five VNTRs from 2007 to 2014. We found that mid ranges of repeat units of 8–14 in VNTR locus STTR5, 6–13 in STTR6, and 9–12 in STTR10 were always predominant in the population (>50%). In vitro passaging experiments using MLVA type carrying extreme length alleles found that the majority of long length alleles mutated to short ones and short length alleles mutated to longer ones. Both data suggest directional mutability of VNTRs toward mid-range repeats. Sequencing of 28 isolates from a newly emerged MLVA type and its five single locus variants revealed that single nucleotide variation between isolates with up to two MLVA differences ranged from 0 to 12 single nucleotide polymorphisms (SNPs). However, there was no relationship between SNP and VNTR differences. A population genetic model of the joint distribution of VNTRs and SNPs variations was used to estimate the mutation rates of the two markers, yielding a ratio of 1 VNTR change to 6.9 SNP changes. When only one VNTR repeat difference was considered, the majority of pairwise SNP difference between isolates were 4 SNPs or fewer. Based on this observation and our previous findings of SNP differences of outbreak isolates, we suggest that investigation of S. Typhimurium community outbreaks should include cases of 1 repeat difference to increase sensitivity. This study offers new insights into the short-term VNTR evolution of S. Typhimurium and its application for epidemiological typing.

Highlights

All bacterial genomes contain repetitive DNA in multiple loci called variable-number tandemrepeat (VNTR) (van Belkum, 2007)
For the remaining 3 variable number of tandem repeat (VNTR) loci, the distribution of the size of repeat units largely followed a normal distribution, with the median size having the highest frequency by both number of MLVA types and the total number of isolates (Figures 1C–E)
The top 10 MLVA types vary from year to year from less than 1% to over 20%, which account for 32.6% of total isolates (Table 2)

Summary

Introduction

All bacterial genomes contain repetitive DNA in multiple loci called variable-number tandemrepeat (VNTR) (van Belkum, 2007). Due to their high variability and ease of detection, VNTRs are useful markers for epidemiological studies. Since a small number of MLVA types dominate, which we refer to as endemic MLVA types, the discriminatory power of MLVA is significantly reduced for outbreak investigations when they are caused by endemic MLVA types as the same MLVA type can potentially be found in epidemiologically unlinked cases (Sintchenko et al, 2012). Recovery of five or more geographically clustered isolates of the same MLVA type within a 4-week window period has been used as a trigger for public health investigation (Sintchenko et al, 2012)

Methods

Results

Discussion

Conclusion