Isolation and characterization of lytic bacteriophages targeting major multi-drug resistant high-risk clones of carbapenemase-producing Klebsiella pneumoniae

Klebsiella pneumoniae (Kpn) is a major cause of serious healthcare-associated infections often associated to high mortality rates. The species has a remarkable propensity to become resistant to a wide number of antibiotics, both by acquisition of exogenous resistance genes and by accumulation of chromosomal mutations. These features, together with the ability to rapidly disseminate in hospital settings causing even large outbreaks, make Kpn one of the most worrisome Gram-negative opportunistic pathogen. Here we describe three novel lytic bacteriophages targeting major clonal lineages of Kpn, namely those belonging to Clonal Group (CG)258 clade I, CG258 clade II, CG101 and CG307. Hospital wastewaters were screened for the presence of bacteriophages. The obtained bacteriophages were characterized by determination of host-range, structure (by transmission electron microscopy), whole DNA sequencing, stability to physicochemical conditions, and their efficacy in protecting larvae of Galleria mellonella from death caused by K. pneumoniae infection. All bacteriophages were composed by a dsDNA genome. One bacteriophage belonged to the Podoviridae family, while the others to the Myoviridae family. Each bacteriophage selectively targeted specific Kpn clones and was able to protect larvae of G.mellonella from death in an experimental infection model, even when challenged with colistin-resistant or hypermucoviscous strains.