Development of a core genome multilocus sequence typing scheme and life identification number code classification...

Staphylococcus aureus infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates the treatment of S. aureus infections. Understanding the population structure and distribution of genetic lineages of S. aureus is central to understanding the biology, epidemiology and pathogenesis of this organism. This study exploited a large, publicly available dataset of nearly 27,000 S. aureus 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 S. aureus 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 S. aureus genomes. This S. aureus cgMLST scheme and LIN code system is a high-resolution, stable genotyping tool that enables detailed genomic analyses of S. aureus.