Cross-Kingdom Infection of Macrophages Reveals Pathogen- and Immune-Specific Global Reprogramming and Adaptation

The interactions between a host and microbe drive the health and disease status of the host. Of importance is the cause of dysbiosis in the presence of a pathogen, and critically, the relationship between the host and pathogen may evolve over time through response and adaptation. For immunocompromised individuals, dual infections are prevalent and contribute to disease severity and treatment options. Here, we explore the global reprogramming of host cells in response to immediate and established microbial infections with the human fungal pathogen Cryptococcus neoformans and the nosocomial bacterial pathogen Klebsiella pneumoniae. Using quantitative proteomics, we uncovered cross-kingdom protein-level changes associated with initial fungal infection, followed by a remarkable adaptation of the host and pathogen to a dormant state. This stabilization is disrupted over time upon bacterial infection, with the production of virulence-associated bacterial proteins and severely altered host response. We support our findings with the profiling of two major virulence determinants in C. neoformans, catalase and melanin, which demonstrate an interconnected regulation in response to both host defense and bacterial invasion. Overall, we report novel fungal and bacterial modulation of the host, including adaptation and stabilization, suggesting an opportunity to effectively treat dual infections by selectively targeting proteins critical to the host's infection stage. IMPORTANCE The relationship between the human microbiota and infectious disease outcome is a rapidly expanding area of study. Understanding how the host responds to changes in its symbiotic relationship with microbes provides new insight into how disruption can promote disease. In this study, we investigated the evolving relationship between innate immune cells of the host during immediate and established infections with fungal and bacterial pathogens, commonly observed within the lungs of immunocompromised individuals. We observed critical reprogramming of each biological system over time and in response to the changing environment, which influences microbial virulence. The goal of this important work is to improve our fundamental understanding of pathogenesis, as well as the regulatory relationships between hosts and microbes that drive disease outcome. We envision defining improved therapeutic treatment options for the host dependent on disease state to reduce the global impact and burden of infectious diseases, especially in the face of ever-increasing rates of antimicrobial resistance.