Harnessing phage resistance mechanisms for optimization of antibiotic therapy in mycobacteria

Oregon State University received a $408,375 Project Grant award on July 14, 2025, from the National Institute of Allergy and Infectious Diseases under the Allergy and Infectious Diseases Research program (CFDA 93.855) to conduct research on phage-antibiotic combination therapies for treating Mycobacterium abscessus (MAB) infections. The research deliverables focus on identifying and characterizing MAB surface targets involved in phage resistance mechanisms and elucidating the interaction mechanisms between phages and mycobacteria. The project aims to generate fundamental knowledge regarding fitness trade-offs between phage resistance and antibiotic resistance, with the ultimate objective of developing optimized phage formulations that can synergize with antibiotic treatments to enhance clinical outcomes in difficult-to-manage MAB cases, particularly for cystic fibrosis patients.

The two-year project, concluding June 30, 2027, will deliver research outputs addressing the gap between effective in vitro antibiotic activity and unpredictable clinical treatment outcomes for MAB infections. By investigating how bacterial surface factors contribute to distinct phage resistance mechanisms and the associated fitness costs, the research will provide translational insights for designing therapeutic phage formulations that leverage the demonstrated synergistic benefits of phage-antibiotic combination treatments over single-agent therapies. This research aligns with the program's objectives to advance scientific knowledge of infectious disease mechanisms and develop innovative therapeutic interventions.

Abstract

Mycobacterium abscessus (MAB) is emerging as a clinically important pathogen associated with infections in immunocompromised as well as healthy individuals. MAB incidents have been increasing worldwide leading to high morbidity and fatality rates. While clinically available antibiotics effectively kill MAB in vitro, despite of combinational and lengthy antimicrobial regimens, treatment outcomes in clinics are unpredictable and often ineffective, demanding the use of novel therapies and technologies for improved results. Phage therapy is one of the promising alternatives under development for cystic fibrosis patients that has been successfully used during difficult to manage cases such as multidrug-resistant and disseminated infections of MAB. Moreover, phage- antibiotic combination treatments have been shown to be more effective over the use of single agents. The current use of therapeutic phages in humans is limited to lytic phages that can efficiently lyse and inhibit the growth of the host bacteria. However, substantial research demonstrates that lytic phages can steer the evolution of phage resistance in bacteria at a cost of increased vulnerability to antibiotics and immune system, diminishing bacterial virulence in the mammalian host. The overall goal of this application is to deepen the fundamental understanding of phage biology by elucidating the interaction mechanisms with mycobacteria and assessing the fitness costs linked to the trade-offs between phage resistance and antibiotic resistance. This knowledge will be applied toward the translational goal of this proposal for designing phage formulations that can synergize antibiotic action, ultimately enhancing clinical outcomes. Therefore, in the aim 1A, we will identify MAB surface targets involved in distinct phage resistance mechanisms. Our central hypothesis is that bacterial surface factors contributing to phage resistance can compromise the integrity of the mycomembrane and reduce the functionality of mycobacterial surface targets involved in antibiotic intrinsic resistance. By finding phages that can drive diverse pleiotropic effects, we aim to sensitize MAB to conventional antibiotics via phage-antibiotic combination therapy. In the aim 1B, we will validate trade-offs between phage and antibiotic resistance and evaluate increased efficacy of antibiotics in drug-susceptible and drug-resistant MAB isolates through the use of phages. The new knowledge gained from this proposal will directly inform the rational design of phage cocktails and phage-antibiotic combinations, enhancing the clinical efficacy of current antimicrobials.