K. pneumoniae ST258 genomic variability and bacteriophage susceptibility

Venturini, C.; Ben Zakour, N.; Bowring, B.; Morales, S.; Cole, R.; Kovach, Z.; Branston, S.; Kettle, E.; Thomson, N.; Iredell, J.

doi:10.1101/628339

bioRxiv · 10.1101/628339

K. pneumoniae ST258 genomic variability and bacteriophage susceptibility

Venturini, C.·Ben Zakour, N.·Bowring, B.·Morales, S.·Cole, R.·Kovach, Z.·Branston, S.·Kettle, E.·Thomson, N.·Iredell, J.

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Abstract

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

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Venturini, C., Ben Zakour, N., Bowring, B., Morales, S., Cole, R., Kovach, Z., Branston, S., Kettle, E., Thomson, N., Iredell, J.. 2019-05-05. K. pneumoniae ST258 genomic variability and bacteriophage susceptibility. https://doi.org/10.1101/628339

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