Mimee, Mark | Search NASA

DOE OSTI2024

Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae

Antibiotic use can lead to the expansion of multi-drug-resistant pathobionts within the gut microbiome that can cause life-threatening infections. Selective alternatives to conventional antibiotics are in dire need. Here, in this work, we describe a Klebsiella PhageBank for the tailored design of bacteriophage cocktails to treat multi-drug-resistant Klebsiella pneumoniae. Using a transposon library in carbapenem-resistant K. pneumoniae, we identify host factors required for phage infection in major Klebsiella phage families. Leveraging the diversity of the PhageBank, we formulate phage combinations that eliminate K. pneumoniae with minimal phage resistance. Optimized cocktails selectively suppress the burden of K. pneumoniae in the mouse gut and drive the loss of key virulence factors that act as phage receptors. Phage-mediated diversification of bacterial populations in the gut leads to co-evolution of phage variants with higher virulence and broader host range. Altogether, the Klebsiella PhageBank charts a roadmap for phage therapy against a critical multidrug-resistant human pathogen.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Rapid Design and Engineering of Smart and Secure Microbiological Systems (Final Report)

The design and application of successfully engineered biosystems requires an understanding of how engineered microbes will interact with other organisms – either as one-on-one competitors or in the context of microbial consortia. Engineering microorganisms from first principles for non-laboratory, environmental applications is inherently challenging because: (1) engineered systems tend to quickly revert back to their wild-type behaviors; and (2) these systems typically pay a price in reduced fitness, making them uncompetitive against invasive contaminating species (i.e., metabolic burden). For this project, we used a synthetic biology-based strategy to investigate the organization, control, stabilization, and destabilization of natural and engineered microbes. This approach enabled development of (1) single-strain systems capable of detecting and responding to target organisms in the environment; (2) a pipeline for refining and engineering biological constructs in new, non-model host organisms; and (3) improved systems for rapidly designing, engineering, and assaying new biological modules. This coupled approach to safeguard system design is predictable and portable across bacterial species and is focused on microbes that are part of the beneficial plant microbiome. A long-term goal beyond the proposed research is to enable the rational engineering of microbial communities based on first principles of biological design that mimic the smart performance of microorganisms observed in natural systems.

59 BASIC BIOLOGICAL SCIENCES↗