A Photoconvertible Reporter System for Bacterial Metabolic Activity Reveals That Staphylococcus aureus Enters a Dormant-Like State to Persist within Macrophages

Staphylococcus aureus is a leading cause of difficult-to-treat infections. The capacity of S. aureus to survive and persist within phagocytic cells is an important factor contributing to therapy failures and infection recurrence. Therefore, interfering with S. aureus intracellular persistence is key to treatment success. In this study, we used a S. aureus strain carrying the reporter mKikumeGR that enables the monitoring of the metabolic status of intracellular bacteria to achieve a better understanding of the molecular mechanisms facilitating S. aureus survival and persistence within macrophages. We found that shortly after bacteria internalization, a large fraction of macrophages harbored mainly S. aureus with high metabolic activity. This population decreased gradually over time with the concomitant increase of a macrophage subpopulation harboring S. aureus with low metabolic activity, which prevailed at later times. A dual RNA-seq analysis performed in each macrophage subpopulation showed that the host transcriptional response was similar between both subpopulations. However, intracellular S. aureus exhibited disparate gene expression profiles depending on its metabolic state. Whereas S. aureus with high metabolic activity exhibited a greater expression of genes involved in protein synthesis and proliferation, bacteria with low metabolic activity displayed a higher expression of oxidative stress response-related genes, silenced genes involved in energy-consuming processes, and exhibited a dormant-like state. Consequently, we propose that reducing metabolic activity and entering into a dormant-like state constitute a survival strategy used by S. aureus to overcome the adverse environment encountered within macrophages and to persist in the intracellular niche. IMPORTANCE The capacity of Staphylococcus aureus to survive and persist within phagocytic cells has been associated with antibiotic treatment failure and recurrent infections. Here, we investigated the molecular mechanisms leading to S. aureus persistence within macrophages using a reporter system that enables to distinguish between intracellular bacteria with high and low metabolic activity in combinstion with a dual RNA-seq approach. We found that with the progression of infection, intracellular S. aureus transitions from a high metabolic state to a low metabolic dormant-like state by turning off major energy-consuming processes while remaining viable. This process seems to be driven by the level of stress encountered in the intracellular niche. Our study indicates that effective therapies by which to treat S. aureus infections should be able to target not only high metabolic bacteria but also intracellular dormant-like S. aureus. The capacity of Staphylococcus aureus to survive and persist within phagocytic cells has been associated with antibiotic treatment failure and recurrent infections. Here, we investigated the molecular mechanisms leading to S. aureus persistence within macrophages using a reporter system that enables to distinguish between intracellular bacteria with high and low metabolic activity in combinstion with a dual RNA-seq approach.