Development of a core genome multilocus sequence typing scheme and life identification number code classification system for Staphylococcus aureus

<i>Staphylococcus aureus</i> infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates the treatment of <i>S. aureus</i> infections. Understanding the population structure and distribution of genetic lineages of <i>S. aureus</i> is central to understanding the biology, epidemiology and pathogenesis of this organism. This study exploited a large, publicly available dataset of nearly 27,000 <i>S</i>. <i>aureus</i> genomes to (i) develop a core genome multilocus sequence typing (cgMLST) scheme, (ii) stratify hierarchical clusters based on allelic similarity thresholds, and (iii) define the clusters with a life identification number (LIN) code classification system. The cgMLST scheme characterised allelic variation at 1,716 core gene loci, and 13 classification thresholds were defined, which discriminated <i>S. aureus</i> variants across a range of genetic similarity thresholds. LIN code 'lineages' and clonal complexes defined by seven-locus multilocus sequence typing were highly concordant, but the LIN codes permitted a wider range of genetic discrimination among <i>S. aureus</i> genomes. This <i>S. aureus</i> cgMLST scheme and LIN code system is a high-resolution, stable genotyping tool that enables detailed genomic analyses of <i>S. aureus</i>.