Discovery of novel gut-derived <i>Klebsiella pneumoniae</i> phages and mucus-interacting gut phage proteins

Abstract

The rise in antimicrobial resistance and the stagnation in antibiotic development have intensified interest in alternative therapies. Bacteriophages, viruses of bacteria, have significant potential, for both classical phage therapy and for microbiome modulation. Klebsiella pneumoniae is a high-risk pathogen due to its multidrug resistance and virulence, causing acute tissue infections as well as chronic gut colonisations that may drive other diseases, like inflammatory bowel disease (IBD). Consequently, Klebsiella phages are highly sought after, yet their therapeutic application is hindered by key gaps, including the lack of standardised accessible phage and strain collections, limited understanding of the roles of Klebsiella in IBD, and poor knowledge of phage ecology in the gut. To address these, this thesis showcases the establishment of KlebPhaCol, an open-source collection of 52 newly isolated Klebsiella phages and 74 Klebsiella strains, including clinical and reference strains. This resource includes gut-relevant phages infecting the IBD-associated K. pneumoniae ST323 strain and enables the centralised study of Klebsiella-phage interactions. It further explores the nematode Caenorhabditis elegans as a simple in vivo model for Klebsiella-driven gut inflammation, and investigates phage ecology within the intestinal mucosa, commonly disrupted in IBD. Our findings reveal genomic and functional features of KlebPhaCol, including the discovery of a novel phage family linked to the gut environment, Felixviridae. We also show Klebsiella induces intestinal distension in C. elegans, suggesting a tractable model for studying Klebsiella-driven inflammation. Finally, we uncover a repertoire of 6,302 putative phage-encoded mucus-interacting proteins, many with evidence of bacterial origin and plausible retained functionality as well as 390 hits derived from Klebsiella phages, offering insights on potential mechanisms by which Klebsiella spp. may achieve gut colonisation and contribute to disease. In conclusion, this thesis lays foundational resources and insights into Klebsiella-phage interactions, advancing phage therapy developments and deepening the understanding of phage ecology in the gut