Cell-free production of personalized therapeutic phages targeting multidrug-resistant bacteria

Quirin Emslander, Kilian Vogele, Peter Braun, Jana Stender, Christian Willy, Markus Joppich, Jens A. Hammerl,
Miriam Abele, Chen Meng, Andreas Pichlmair, Christina Ludwig, Joachim J. Bugert, Friedrich C. Simmel, and Gil G. Westmeyer

Cell Chemical Biology https://doi.org/10.1016/j.chembiol.2022.06.003

Abstract

Bacteriophages are potent therapeutics against biohazardous bacteria, which rapidly develop multidrug resistance. However, routine administration of phage therapy is hampered by a lack of rapid production, safe bioengineering, and detailed characterization of phages. Thus, we demonstrate a comprehensive cell-free platform for personalized production, transient engineering, and proteomic characterization of a broad spectrum of phages. Using mass spectrometry, we validated hypothetical and non-structural proteins and could also monitor the protein expression during phage assembly. Notably, a few microliters of a one-pot reaction produced effective doses of phages against enteroaggregative Escherichia coli (EAEC), Yersinia pestis, and Klebsiella pneumoniae. By co-expressing suitable host factors, we could extend the range of cell-free production to phages targeting gram-positive bacteria. We further introduce a non-genomic phage engineering method, which adds functionalities for only one replication cycle. In summary, we expect this cell-free methodology to foster reverse and forward phage engineering and customized production of clinical-grade bacteriophages.