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

Antibiotic usage can lead to expansion of multi-drug resistant pathobionts within the gut microbiome, which can cause life-threatening infections. Alternatives to conventional antibiotics that selectively remove specific taxa are in dire need. Here, we describe a Klebsiella PhageBank that enables the rapid design of antimicrobial bacteriophage cocktails to eliminate multi-drug resistant Klebsiella pneumoniae. Using a transposon library in carbapenem-resistant K. pneumoniae, we identified host factors required for phage infection to inform the design of phage cocktails that mitigate the emergence of resistance. Leveraging the diversity of the PhageBank and experimental evolution strategies, we formulated combinations of phages that effectively eradicate multi-drug resistant K. pneumoniae in vitro and in mouse decolonization models. Further, optimized bacteriophage cocktails not only selectively suppressed the burden of multi-drug resistant K. pneumoniae in the mouse microbiome, but also selected for acapsular, phage-resistant mutants with attenuated virulence properties. The informed design of lytic phage cocktails could thus prove an effective means to both remove pathobionts and to select for beneficial genotypes in a complex microbial community.