Characterizing <i>Staphylococcus aureus</i> genomic epidemiology with multilevel genome typing

<i>Staphylococcus aureus</i> causes both hospital- and community-acquired infections worldwide. Methicillin-resistant <i>S. aureus</i> is best known and has spread across the globe. Whole-genome sequencing (WGS) can type strains at the highest resolution. To enable best use of WGS data for surveillance of <i>S. aureus</i>, this study developed a multilevel genome typing (MGT) scheme that provides a publicly available, standardized, flexible, and easily communicated system to describe <i>S. aureus</i> strains. MGT has eight typing levels that provide progressively higher resolution. Each of these levels allows subtypes to be accurately identified and tracked. We show that MGT can be used to track well-known <i>S. aureus</i> strains at low resolution while simultaneously being able to track outbreaks in hospital settings at high resolution. The <i>S. aureus</i> MGT will facilitate the use of genomic data for surveillance without the need for bioinformatic expertise, improving efforts to control this important pathogen and prevent infections.