Whole genome single nucleotide polymorphism genotyping of Staphylococcus aureus

Changchuan Yin University of Illinois at Chicago Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1908.42001

Next-generation sequencing technology enables the routine detection of bacterial pathogens for clinical diagnostics and genetic research. Whole-genome sequencing has been of importance in the epidemiologic analysis of bacterial pathogens. However, few whole-genome sequencing-based genotyping pipelines are available for practical applications. Here, we present the whole-genome sequencing-based single nucleotide polymorphism(SNP) genotyping method and apply to the evolutionary analysis of methicillin-resistant Staphylococcus aureus. The SNP genotyping method calls genome variants using next-generation sequencing reads of whole genomes and calculates the pair-wise Jaccard distances of the genome variants. The method may reveal the high-resolution whole-genome SNP profiles and the structural variants of different isolates of methicillin-resistant S. aureus(MRSA) and methicillin-susceptible S. aureus(MSSA) strains. The phylogenetic analysis of whole genomes and particular regions may monitor and track the evolution and the transmission dynamic of bacterial pathogens. The computer pro- grams of the whole genome sequencing-based SNP genotyping methods are available to the public at https://github. com/ cyinbox/NGS.
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  title={Whole genome single nucleotide polymorphism genotyping of Staphylococcus aureus},
  author={Changchuan Yin, and Stephen S.-T. Yau},
Changchuan Yin, and Stephen S.-T. Yau. Whole genome single nucleotide polymorphism genotyping of Staphylococcus aureus. 2019. http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20190821024256271998431.
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