Project 3: Functional Microbiome and Host Signatures in Transition from Commensal to pathogen

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ABSTRACT Project 3: Functional Microbiome and Host Signatures in Transition from Commensal to pathogen Overuse of antibiotics and adaptability of bacteria has resulted in antimicrobial resistance (AMR) in pathogens of significant public health concern. Identifying individuals who are susceptible to infection is critical in implementing an effective treatment plan and in promoting good antimicrobial stewardship. This project focuses on developing innovative systems technology to develop microbiome-based risk algorithms that identify susceptible patients in the general hospitalized population. The project premise being tested is that nosocomial pathogens that colonize the intestines specifically target individuals with immature infant-like gut microbiota features that are permissive to pathogen colonization. The notable AMR-pathogens of our study include Clostridioides difficile, vancomycin-resistant enterococcus (VRE), carbapenem-resistant Klebsiella pneumoniae, and extended spectrum β-lactamase producing Enterobacteriacae (ESBL-E/CRE) because these organisms often colonize the intestines before causing infection. Specifically, we show that these priority pathogens often co-colonize vulnerable patients who are missing keystone microbiota species that appear to be broadly protective against these bacteria by producing diverse bacteriocins. In Project 3 of this PO1 application, we will perform synergistic functional profiling of these unique host-microbiota-pathogen interactions to address the following two specific aims: • Aim 3.1. Define the metabolically active microbiota community structure identified with pathogen colonization and disease progression in the susceptible patient. • Aim 3.2. Characterize keystone microbiota features and their protective antimicrobial mechanisms. The study is impactful because we intend to establish predictive microbiome-risk algorithms for precision infection management of immunosuppressed and critically ill patients. The long-term goal is to advise the physician and healthcare stakeholders of clinical surveillance and therapeutic interventions that match the risk posed by each individual’s infection, as well as define host-microbiota-pathogen interactions that are permissive to other emerging infections.