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Understanding Klebsiella pneumoniae respiratory infections

Final Report Summary - U-KARE (Understanding Klebsiella pneumoniae respiratory infections)

U-KARE aimed to gain a holistic understanding of the networks conveying the cross-talk between the human pathogen Klebsiella pneumoniae (KP) and the innate immune system. The isolation of KP strains resistant to "last resort" antimicrobials has significantly narrowed, or in some settings completely removed, the therapeutic options for the treatment of KP infections. This has led to multidrug-resistant KP being singled out as an "urgent threat to human health" by the European Centre for Disease Prevention and Control, the CDC and the WHO. Unfortunately, at present, we cannot identify candidate compounds in late-stage development for treatment of multidrug KP infections; this pathogen is exemplary of the mismatch between unmet medical needs and the current antimicrobial research and development pipeline. Furthermore, there is still scant evidence on KP pathogenesis at the molecular and cellular level. The development of new therapeutic strategies requires a better understanding of KP pathophysiology in the context of the complex interactions between bacterial pathogens and their hosts.

In this research programme, we have identified hitherto unknown strategies employed by a human pathogen to control cell intrinsic immunity. We have provided a comprehensive overview of how KP ablates three key host posttranslational modifications of proteins, SUMOylation, NEDDylation and ISGylation, to limit the activation of inflammatory responses. Mechanistically, our results demonstrate that KP hijacks involved in the homeostatic regulation of these modifications. This strategy is radically different to those employed by other pathogens who deliver bacterial proteins into host cells to modulate a variety of cellular functions. In another pioneering study of the laboratory, we have discovered that KP persists intracellularly in human and mouse macrophages within a unique compartment hence suggesting that KP may exploit macrophages to enhance its survival while avoiding immune control. This breakthrough has important clinical implications since the current therapies against KP are ineffective against intracellular bacteria. Mechanistically, our results demonstrate that KP activates a PI3K-AKT-RAB14 axis to block the lysosome fusion. Aiding in intracellular survival, we have uncovered that KP blocks autophagy by activating mTORC1. Remarkably, KP exploits a TLR4-type I IFN dependent pathway to activate mTORC1. We have provided mechanistic information on how KP blocks JAK-STAT signalling in epithelial cells to limit to the deleterious effects of type I IFN-dependent antimicrobial responses. Notably, we have shown that type I IFN signaling protects against lung infection with KP by launching bacterial growth-controlling interactions between alveolar macrophages and natural killer (NK) cells, illustrating a KP-type I IFN arms race. Our research efforts have already led to the identification of hitherto unknown microbial factors needed for full effectiveness of immune evasion. Our findings demonstrate that KP capsule, lipopolysaccharide (LPS) O-polysaccharide and the pullulanase (PulA) type 2 secretion system (T2SS) perturb TLR-dependent recognition of KP. We have also shown that KP modifies the LPS lipid A moiety in the lungs of infected mice to evade immune surveillance. Notably, this in vivo LPS modification also mediates resistance to colistin, one of the last options to treat multidrug resistant KP. We have also revealed the precise molecular resistance mechanisms of the clinically relevant mgrB mutation leading to resistance to colistin. Our data uncovered that mgrB mutation leads to extensive surface remodelling of KP enhancing KP virulence by decreasing antimicrobial peptide susceptibility and attenuating early host defence response activation, connecting antimicrobial resistance and evasion of immune responses.

This project raised to the challenge of combating multi-resistant infections by improving our understanding of how pathogens exploit the attacks of an activated immune system to enhance their survival. Interference with pathogen virulence and/or signalling pathways hijacked by pathogens for their own benefit is an especially compelling approach, as it is thought to apply less selective pressure for the development of resistance than traditional strategies, which are aimed at killing pathogens or preventing their growth. It is therefore believed that the targets we have validated during the research will lead to new therapeutics.