Comparative Genome Analysis Reveals the Molecular Basis of Niche Adaptation of Staphylococcus epidermidis Strains

Staphylococcus epidermidis is one of the most commonly isolated species from human skin and the second leading cause of bloodstream infections. Here, we performed a large-scale comparative study without any pre-assigned reference to identify genomic determinants associated with the diversity and adaptation of S. epidermidis strains to various environments. Pan-genome of S. epidermidis was open with 435 core proteins and had a pan-genome size of 8,034 proteins. Genome-wide phylogenetic tree showed high heterogeneity and suggested that routine whole genome sequencing was a powerful tool for analyzing the complex evolution of S. epidermidis and for investigating the infection sources. Comparative genome analyses demonstrated a range of antimicrobial resistance (AMR) genes, especially those within mobile genetic elements. The complicated host-bacterium and bacterium-bacterium relationships help S. epidermidis to play a vital role in balancing the epithelial microflora. The highly variable and dynamic nature of the S. epidermidis genome may contribute to its success in adapting to broad habitats. Genes related to biofilm formation and cell toxicity were significantly enriched in the blood and skin, demonstrating their potentials in identifying risk genotypes. This study gave a general landscape of S. epidermidis pan-genome and provided valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible species.