Molecular Mechanisms of Staphylococcus Epidermidis Strain Diversity

PROJECT SUMMARY / ABSTRACT Staphylococcus epidermidis is a ubiquitous member of the human skin and mucosal microbiota. Functionally, it is a key contributor to human health via immune modulation and microbial community homeostasis. Yet the ‘commensal’ S. epidermidis is also an important pathogen and disease risk reservoir—it is the most frequent cause of medical device and bloodstream infections. Multiple phylogenetically diverse subspecies, or strains, of S. epidermidis can co-inhabit the skin with genomes of variable gene content. The overwhelming majority of these genes have unknown function. We hypothesize that this variable gene content, or accessory genome, interacts with core genes to enable strains to uniquely respond to and thrive in different environments, and that mixing of these genetically diverse strains is necessary to maintain a healthy homeostasis in the skin. To investigate the function of these genes and to understand how genetic diversity at the strain level contributes to population-level phenotype, we will functionally profile a set of phylogenetically diverse strains isolated from healthy individuals and individuals with bloodstream infections. We will create CRISPRi tools for gene knockdown in S. epidermidis to systematically identify strain-specific and core genes that underlie the ability to colonize and compete in the skin and infections. Aim 1 develops the CRISPRi genetic toolkit to created pooled S. epidermidis knockdown pools. Phenotypic profiling these pools will greatly expand our knowledge of important commensal strategies employed by a common microbial partner, and how genetic heterogeneity may impact the commensal to infectious transition. Aim 2 investigates the role of strain admixture in this transition. This combination of genomic approaches and mechanistic studies will provide the first investigation into the function of the S. epidermidis pangenome. Annotating inter-strain genetic diversity will reveal new insights into the functional consequence of strain diversity: how strains can successfully transition between commensal and virulence lifestyles, and how multiple strains can co-exist in an ecological network.