Abstract
BackgroundVariable 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 FindingsCapillary 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/SignificanceAppropriate 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.
Highlights
Plague, one of the most devastating infectious diseases in human history, is a reemerging infectious disease causing outbreaks in several areas since the early 1980s
General Features of Variable number of tandem repeats (VNTRs) Loci tandem repeats (TRs) regions are widely distributed in the Y. pestis genome, with 280 alleles of the TRs identified from five published genomes (Figure 1)
VNTRs in Y. pestis and developed a simple genotyping scheme based on the selected ‘‘14+12’’ VNTRs. This hierarchical genotyping method provides enough discrimination power and reduces time and cost substantially. This scheme reduces the possible distortion of homoplasies caused by rapid mutations of VNTR loci
Summary
One of the most devastating infectious diseases in human history, is a reemerging infectious disease causing outbreaks in several areas since the early 1980s. The causative agent of plague, has killed hundreds of millions of people in the three major historical plague pandemics [1,2]. The demand for preparedness for biological terrorism threats and natural plague outbreaks has renewed interest in the detection, identification, and source-tracing of Y. pestis, especially by methods that can determine the origin of the outbreak strain. 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. We probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci
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