Communications in Information and Systems

Volume 19 (2019)

Number 1

Whole genome single nucleotide polymorphism genotyping of Staphylococcus aureus

Pages: 57 – 80



Changchuan Yin (Department of Mathematics, Statistics, and Computer Science, University of Illinois, Chicago, Il., U.S.A.)

Stephen S.-T. Yau (Department of Mathematical Sciences, Tsinghua University, Beijing, China)


Next-generation sequencing technology enables 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 programs of the whole genome sequencing-based SNP genotyping method are available to the public at

This research was supported by National Natural Sciences Foundation of China (31271408 to S.S.-T. Yau) and Tsinghua University start-up research fund (to S.S.-T. Yau). We are grateful to Dr.Donald Morrison at University of Illinois at Chicago and Prof. Jiasong Wang at Nanjing University for insightful discussion and valuable comments. We thank Melissa Yin for collecting genome data. We appreciate two anonymous reviewers for the constructive review so that the research was greatly improved.

Published 18 April 2019