Genome evolution and population dynamics of Staphylococcus bacteria

The gram-positive bacterial genus Staphylococcus (phylum Firmicutes) is a heterogeneous group that consists of commensals and opportunistic pathogens of humans and animals. To date, there are 57 validly published species according to the List of Prokaryotic names with Standing in Nomenclature (LPSN). The most well-studied and widely sampled species is Staphylococcus aureus, which causes a wide range of diseases in humans from relatively minor skin infections to much more invasive and serious sepsis, pneumonia, or endocarditis. For many years, Staphylococcus other than S. aureus have been regarded as non-pathogenic, but these bacteria are now being recognized as potential pathogens in humans. Other species, mainly Staphylococcus epidermidis and Staphylococcus haemolyticus, are members of the skin flora of human; however, they can invade deeper tissues through infection of inserted medical devices. Many other species are frequent colonizers of various species of mammals and birds, yet little is known about the diversity and evolutionary history of these non-aureus species. In this dissertation, I use concepts, approaches and methods in bacterial population genomics to investigate the evolutionary mechanisms that shape the diversity and population structure of Staphylococcus species across different ecological niches: Staphylococcus pseudintermedius in companion animals (Chapter 1), S. aureus in bloodstream infections in humans (Chapter 2), and coagulase-negative Staphylococcus (Chapter 3). Overall, I found that many genomic elements, such as antimicrobial resistance and virulence genes, substantially vary within and between species. Frequent horizontal gene transfer (HGT) shapes this diversity and the adaptation of certain species and strains to certain niches. HGT in Staphylococcus is facilitated by a variety of mobile genetic elements, such as insertion sequences (Chapter 4). Many non-aureus species likely act as major reservoir of genetic variants that can be acquired by S. aureus. Findings from this dissertation will provide important insights to managing and controlling staphylococcal diseases in humans and animals