Whole genome single nucleotide polymorphism genotyping of <i>Staphylococcus aureus</i>

Abstract

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 methicillinsusceptible 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 https://github.com/cyinbox/NGS.

Genotyping coronavirus SARS-CoV-2: methods and implications

“…However, in an emergency time, the complete genomes may not be available for SNP genotyping. In this case, the SNP variant calling process may directly use the raw NGS reads (Yin and Yau, 2019). The SNP variants then can be obtained by mapping the NGS reads to the reference genome by BWA alignments (Li, 2013), followed by GATK variant calling (McKenna et al, 2010).…”

“…Therefore, the genetic distance of two genomes corresponds to the Jaccard distance of their SNP variants. The Jaccard distance of SNP variants was adopted in the phylogenetic analysis of human or bacterial genomes (Comas et al, 2009;Yu et al, 2017;Yin and Yau, 2019). In this study, we use the Jaccard distance of the SNP mutations of virus genomes to measure the dissimilarity of virus isolates.…”

“…Coronavirus-HKU1 has been predominantly reported in children in the United States but less common among adults. Three highly pathogenic coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2, which emerged in 2002, and 2019, respectively, have caused severe respiratory disease and thousands of deaths worldwide (Chen, 2020). SARS-CoV-2 coronavirus harbors a linear single-stranded positive RNA genome.…”