The objective of this work is to create and validate a platform for engineering phage-based antimicrobials that share a common scaffold and are generalizable to target a broad range of bacterial pathogens, which we call phagebodies. Our phagebody technology will be used to create efficacious, well-defined, and targeted antimicrobials against carbapenem-resistant Enterobacteriaceae (CRE). CRE are resistant to nearly all antibiotics, and thus there is a tremendous unmet clinical need for new anti-CRE treatment strategies. Bacteriophages enact targeted killing of specific bacteria without affecting neighboring bacteria. These narrow-spectrum agents differ significantly from most chemical antibiotics, which exhibit broad-spectrum activity and can therefore generate undesirable side effects such as Clostridium difficile overgrowth and selection for antibiotic resistance. Furthermore, the antibiotic pipeline for pathogens such as CRE is dwindling. However, for narrow-spectrum agents such as phages to be useful in clinical settings, technologies for the extensible and high-throughput creation of targeted phage therapeutics are critically needed. In conventional phage therapy, cocktails of naturally isolated phages are constructed to cover a broad set of a given target bacteria. This approach poses several difficulties for the use of phage therapy in Western clinical settings. Natural phage cocktails are often composed of phages from diverse families, thus posing challenges for characterization and manufacturing under conditions needed for clinical application. In addition, natural phage isolation protocols are reliant on environmental sampling and screening, which can be laborious and challenging to scale to cover a broad range of perpetually evolving bacterial targets. Here, we will create and optimize a novel strategy for engineering well-defined and customizable phagebodies as antimicrobials. In preliminary studies, we have shown that common phage scaffolds can be retargeted against new bacterial hosts by modular tail fiber swapping or mutagenesis of host-recognition domains within tail fiber tips. We will extend these findings to create highly diversified phage banks that will be screened against panels of carbapenem-resistant E. coli and K. pneumoniae to identify efficacious phages that kill these bacteria. These phages shall be validated and optimized within in vitro and in vivo models of infection. This work is significant since it will provide an extensible technological platform to discover effective phage-based antimicrobials that can be further advanced into preclinical and clinical development against urgent threats, such as CRE and other pathogens. This work is innovative since it involves the novel creation of tailored phagebody antimicrobials that overcome prior challenges associated with natural phage therapy.

Public Health Relevance

The proposed research is relevant to public health because it will generate novel phage-based antimicrobials that combat carbapenem-resistant Enterobacteriaceae (CRE), which are resistant to almost all antibiotics. There is a large unmet clinical need for effective anti-CRE therapies that are well-defined, targeted, and effective. By engineering a generalizable and rapidly adaptable technology for creating effective anti-CRE phages, this project advances the NIH's mission to foster innovative non-traditional therapeutics that advance human health and reduce the impact of infectious diseases.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Exploratory/Developmental Grants Phase II (R33)
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Special Emphasis Panel (ZAI1)
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Xu, Zuoyu
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Massachusetts Institute of Technology
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United States
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