A novel PCR method targeting staphostatin genes differentiates Staphylococcus aureus from Staphylococcus epidermidis in clinical isolates and nasal microbiome samples

Abstract Staphylococcus aureus is a pathogen associated with community-acquired and healthcare-associated infections, and is known for rapid acquisition of resistance to multiple antibiotics. Staphylococcus epidermidis is another staphylococcal species commonly seen as a commensal, but may cause opportunistic infections. These two closely related species may naturally co-colonize and inhabit the human skin and nose; thus it is important to develop methods to differentiate between them. Conventional differentiation methods (e.g., mannitol salt agar, coagulase test, Analytical Profile Index kits) require culturing and isolating the bacteria, while molecular methods based on polymerase chain reaction (PCR) or sequencing are culture independent, highly accurate, and sensitive. They may be objectively interpreted and can be adapted for high-throughput assays. Here, we aimed to develop a rapid and accurate method to differentiate mixtures of S. aureus and S. epidermidis in clinical isolates and microbiome samples. Using comparative genomics tools (e.g., MetaRef and PATRIC bioinformatics resource center), we compared the core and pan genomes of S. aureus and S. epidermidis to determine signature genes for each species. Among candidate genes, we chose the virulence genes, staphostatin B and staphostatin A as genetic biomarkers for S. aureus and S. epidermidis, respectively. We designed PCR primers that target specific sequences within each gene and tested them on DNA isolated from laboratory strains, clinical isolates, nasal isolates, and nasal swabs. Our developed method is simple, specific, sensitive, and can be applied to metagenomic samples as well as competition or co-evolution studies in which the two organisms are co-cultured.