Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme

Yanjun Li; Yujun Cui; Baizhong Cui; Yanfeng Yan; Xianwei Yang; Haidong Wang; Zhizhen Qi; Qingwen Zhang; Xiao Xiao; Zhaobiao Guo; Cong Ma; Jing Wang; Yajun Song; Ruifu Yang

doi:10.1371/journal.pone.0066567

Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme

PLoS One. 2013 Jun 21;8(6):e66567. doi: 10.1371/journal.pone.0066567. Print 2013.

Authors

Yanjun Li¹, Yujun Cui, Baizhong Cui, Yanfeng Yan, Xianwei Yang, Haidong Wang, Zhizhen Qi, Qingwen Zhang, Xiao Xiao, Zhaobiao Guo, Cong Ma, Jing Wang, Yajun Song, Ruifu Yang

Affiliation

¹ State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China ; Laboratory Department, Navy General Hospital, Beijing, China.

Abstract

Background: Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.

Methodology/principal findings: Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.

Conclusions/significance: Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.

MeSH terms

Genetic Loci*
Genetic Variation*
Genotype*
Genotyping Techniques / methods*
Tandem Repeat Sequences*
Yersinia pestis / classification
Yersinia pestis / genetics*

Grants and funding

This work was funded by the State Key Development Program for Basic Research of China (2009CB522601), the National Key Program for Infectious Diseases of China (2012ZX10004215), the Industry Research Special Foundation of China Ministry of Health (201202021), and the National Natural Science Foundation of China (31071111 and 31000015). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.