24Multidrug resistant carbapenemase-producing Klebsiella pneumoniae capable of causing 25 severe disease in humans is classified as an urgent threat by health agencies worldwide. 26 Bacteriophages are being actively explored as potential therapeutics against these multidrug 27 resistant pathogens. We are currently developing bacteriophage therapy against carbepenem-28 resistant K. pneumoniae belonging to the genetically diverse, globally disseminated clonal 29 group CG258. In an effort to define a robust experimental approach for effective selection of 30 lytic viruses for therapy, we have fully characterized the bacterial genomes of 18 target 31 strains, tested them against novel lytic bacteriophages, and generated phage-susceptibility 32 profiles. The genomes of K. pneumoniae isolates carrying blaNDM and blaKPC were sequenced 33 and isolates belonging to CG258 were selected for susceptibility testing using a panel of lytic 34 bacteriophages (n=65). The local K. pneumoniae CG258 population was dominated by 35 isolates belonging to sequence type ST258 clade 1 (86%). The primary differences between 36 ST258 genomes were variations in the capsular locus (cps) and in prophage content. We 37 showed that CG258-specific lytic phages primarily target the capsule, and that successful 38 infection is blocked in many, post-adsorption, by immunity conferred by existing prophages.
39Five bacteriophages specifically active against K. pneumoniae ST258 clade 1 (n=5) 40 belonging to the Caudovirales order were selected for further characterization. Our findings 41 show that effective control of K. pneumoniae CG258 with phage will require mixes of 42 diverse lytic viruses targeting all relevant cps variants and allowing for variable prophage 43 content. These insights will facilitate identification and selection of therapeutic phage 44 candidates against this serious pathogen. 45 46 47 48 Importance 49Bacteriophages are natural agents that exclusively and selectively kill bacteria and have the 50 potential to be useful in the treatment of multidrug resistant infections. K. pneumoniae 51 CG258 is a main agent of life-threatening sepsis that is often resistant to last-line antibiotics.
52Our work highlights some key requirements for developing bacteriophage preparations 53 targeting this pathogen. By defining the genomic profile of our clinical K. pneumoniae 54 CG258 population and matching it with bacteriophage susceptibility patterns, we found that 55 bacteriophage ability to lyse each strain correlates well with K. pneumoniae CG258 structural 56 subtypes (capsule variants). This indicates that preparation of bacteriophage therapeutics 57 targeting this pathogen should aim at including phages against each bacterial capsular 58 subtype. This necessitates a detailed understanding of the diversity of circulating isolates in 59 different geographical areas in order to make rational therapeutic choices. 60 61 62 Klebsiella pneumoniae is an important ubiquitous Gram-negative species capable of causing 63 disease in both humans an...