Klebsiella anti-immunology: exploiting proteins with a eukaryotic SEFIR domain
Lead Research Organisation:
Queen's University Belfast
Department Name: Sch of Medicine, Dentistry & Biomed Sci
Abstract
Our struggle against infectious diseases is far from over. Globalization has increased the risk of pandemics, and the rise of antibiotic-resistant microbes threatens to render existing drugs useless. Public Health England has calculated that the lack of effective antibiotics will render more than the three million operations and cancer treatments life threatening, and more than 90,000 people are estimated to die in the UK over the next 30 years due to antibiotic resistant infections. Of particular concern is the mounting prevalence of respiratory infections caused by Gram-negative bacteria, in particular Klebsiella pneumoniae (the focus of this project), with a 12% increased in incidence in the last five years only in the UK.This is particularly alarming given the high rates of resistance to empirical antibiotics commonly recommended for Klebsiella treatment. In fact, the increasing isolation of strains resistant to "last resort" antimicrobials has significantly narrowed, or in some settings completely removed, the therapeutic options for the treatment of Klebsiella infections. Not surprisingly, this pathogen has been singled out as an "urgent threat to human health" by the UK Government, the U.S. Centers for Disease Control and Prevention, and the World Health Organization due to extremely drug resistant strains. Unfortunately, at present, we cannot identify candidate compounds in late-stage development for treatment of multidrug Klebsiella infections; this pathogen is exemplary of the mismatch between unmet medical needs and the current antimicrobial research and development pipeline. Worryingly, recent studies have alerted that several Klebsiella virulent and multidrug resistant isolates have access to a mobile pool of virulence and antimicrobial resistance genes; hence making possible the emergence of a multidrug resistant, hypervirulent K. pneumoniae isolate capable of causing untreatable infections in healthy individuals. However, our understanding of Klebsiella pathogenesis still contains considerable gaps thereby making a compelling case to better understand Klebsiella infection biology in the context of the complex interactions between bacterial pathogens and their hosts.
In this proposal, by combining the distinct but synergistic expertise across the disciplines of molecular and cellular microbiology, immunology and biochemsitry of the Bengoechea, Moynagh and Schroeder laboratories, we will uncover a hitherto unknown Klebsiella immune evasion strategy directed to blunt IL17-governed host defenses, which have been shown to be essential for the clearance of Klebsiella infections. Our research will reveal that this immune evasion strategy also attenuates host defense signalling launched upon activation of the receptors implicated in sensing infections. Collectively, this proposal will shed new light into the sophisticated means exploited by pathogens to overcome host defenses while opening new opportunities to develop new antimicrobial therapeutics. 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. There is extensive research on the pathways targeted by Klebsiella, and new drugs are currently under development. We anticipate that the outcomes of this proposal would lead to test these drugs in pre-clinical models of klebsiella disease, hence allowing a potential fast-track transition from the basic research to clinical development.
In this proposal, by combining the distinct but synergistic expertise across the disciplines of molecular and cellular microbiology, immunology and biochemsitry of the Bengoechea, Moynagh and Schroeder laboratories, we will uncover a hitherto unknown Klebsiella immune evasion strategy directed to blunt IL17-governed host defenses, which have been shown to be essential for the clearance of Klebsiella infections. Our research will reveal that this immune evasion strategy also attenuates host defense signalling launched upon activation of the receptors implicated in sensing infections. Collectively, this proposal will shed new light into the sophisticated means exploited by pathogens to overcome host defenses while opening new opportunities to develop new antimicrobial therapeutics. 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. There is extensive research on the pathways targeted by Klebsiella, and new drugs are currently under development. We anticipate that the outcomes of this proposal would lead to test these drugs in pre-clinical models of klebsiella disease, hence allowing a potential fast-track transition from the basic research to clinical development.
Technical Summary
As a result of the pressure imposed by the immune system, pathogens have evolved sophisticated methods to overcome innate immune mechanisms. Many bacterial pathogens rely on immune-regulatory proteins blocking the activation of a small number of transcriptional factors, NF-kB, MAPKs, IRFs, which control the activation of host defense mechanisms. In this project, by exploiting the power of cellular microbiology and in vivo models, we will expose a bacterial immune evasion strategy based on prokaryotic proteins with eukaryotic domains to block the essential receptor-adaptor interaction. We will provide compelling evidence demonstrating that Klebsiella pneumoniae exploits an effector protein with a SEFIR domain, found in proteins of the IL17 signalling pathway, to antagonize host defenses. This proposal leverages the expertise of the Bengoechea, Moynagh and Schroeder laboratories on Klebsiella infection biology, innate immune signalling and effector biology, respectively, to provide mechanistic insights into (i) how pathogens undermine IL17 signalling, and (ii) how they control immune responses and cell-autonomous immunity. Altogether, our research will place Klebsiella as a cell biologist manipulating early events of innate immune signalling. K. pneumoniae is been recognized as an "urgent threat to human health", making imperative to to better understand its infection biology to design new strategies to treat Klebsiella infections. The findings of this proposal may serve as the foundation for novel therapeutic and prevention strategies based on enhancing innate host resistance to infection, and ameliorating pathophysiological tissue destruction.
Planned Impact
Who will benefit from this research? Academics will be the main short to medium term beneficiary, as the research will provide knowledge to understand how pathogens counteract the activation of host defenses. This is one of the most competitive areas of research in the field of microbial pathogenesis and immunology. The main collaborative interactions will be groups interested on Klebsiella (Dr Kat Holt and Dr Sylvain Brisse), and international consortia such as the Norwegian Klebsiella network (http://nor-kleb.net/) and the JPIAMR SPARK project (Spread of Population-wide Antibiotic Resistance in Klebsiella). We anticipate exciting new collaborations with groups focusing on systems delivering bacterial effectors, and on proteins with eukaryotic domains. The research will enhance the career development of Dr sa Pessoa (named researcher). Dr. sa Pessoa was responsible for a significant amount of the background research. Industry: The growing number of organisms resistant to available antibiotics has become a public health threat worldwide, being Klebsiella a paradigm of an emerging pathogen. There are already drugs under development targeting the signalling pathways manipulated by Klebsiella which can be tested in our pre-clinical infection models. This will allow a fast-track transition from the basic research to clinical development. Public bodies: The project and the information generated may benefit UK based government bodies such as the Chief Medical Officer, the Dept of Health, and the Dept for Environment, Food and Rural Affaires as the data will provide an evidence-base for policy developments. This proposal is aligned with the strategic action "supporting the development of new antimicrobials and alternative treatments" outline in the UK antimicrobial resistance strategy 2013- 2018. General public: Infections are one of the major global threats that are unfortunately very likely to become more urgent in the near future. It is not appropriate to generate an atmosphere of fear since medical care in UK is at a very high level. However, it is advisable to increase public awareness about the potential threats and to provide the UK national regulatory bodies with a top-class knowledge platform to maintain the unique position of UK as an area of research excellence on infection biology.
How will they benefit from this research?: Knowledge of value to the academic sector will be communicated by publication in peer-reviewed journals, oral and poster presentations at conferences and via invited lectures. Pre prints will be deposited in bioRxiv archive. Exchange of staff and students will promote knowledge transfer between collaborative groups. Staff working on the project will receive training on complementary skills (group management, know-how transfer, and entrepreneurship) which together with the cutting-edge research training received will give Dr sa Pessoa all options for either an excellent career in academia, industry, or to develop a business plan for their own start-up enterprise. Knowledge transfer to industry on new therapeutics to treat infections might have economic potential since royalty payments can reach numbers in the magnitude of several millions or tens of millions. This new treatment(s) will benefit the UK health system. The grant will have impact on the wider public sector by continuing our program of scientific communication. The laboratory hosts undergraduates to engage them in the fundamentals of scientific research. Social media will be targeted via Twitter (@josebengoechea, @gunnar_ns). Queen's University Belfast and the Institute web pages will be additional channels to promote this BBSRC-funded research.
How will they benefit from this research?: Knowledge of value to the academic sector will be communicated by publication in peer-reviewed journals, oral and poster presentations at conferences and via invited lectures. Pre prints will be deposited in bioRxiv archive. Exchange of staff and students will promote knowledge transfer between collaborative groups. Staff working on the project will receive training on complementary skills (group management, know-how transfer, and entrepreneurship) which together with the cutting-edge research training received will give Dr sa Pessoa all options for either an excellent career in academia, industry, or to develop a business plan for their own start-up enterprise. Knowledge transfer to industry on new therapeutics to treat infections might have economic potential since royalty payments can reach numbers in the magnitude of several millions or tens of millions. This new treatment(s) will benefit the UK health system. The grant will have impact on the wider public sector by continuing our program of scientific communication. The laboratory hosts undergraduates to engage them in the fundamentals of scientific research. Social media will be targeted via Twitter (@josebengoechea, @gunnar_ns). Queen's University Belfast and the Institute web pages will be additional channels to promote this BBSRC-funded research.
Organisations
Publications
Bengoechea JA
(2020)
SARS-CoV-2, bacterial co-infections, and AMR: the deadly trio in COVID-19?
in EMBO molecular medicine
Calderon-Gonzalez R
(2024)
In vivo single-cell high-dimensional mass cytometry analysis to track the interactions between Klebsiella pneumoniae and myeloid cells
in PLOS Pathogens
Coya JM
(2022)
Cooperative action of SP-A and its trimeric recombinant fragment with polymyxins against Gram-negative respiratory bacteria.
in Frontiers in immunology
Feriotti C
(2022)
Klebsiella pneumoniae hijacks the Toll-IL-1R protein SARM1 in a type I IFN-dependent manner to antagonize host immunity.
in Cell reports
López-Rodríguez JC
(2023)
Type I interferons drive MAIT cell functions against bacterial pneumonia.
in The Journal of experimental medicine
Odendall C
(2022)
Meeting report - Cell dynamics: host-pathogen interface.
in Journal of cell science
Sá-Pessoa J
(2023)
A trans-kingdom T6SS effector induces the fragmentation of the mitochondrial network and activates innate immune receptor NLRX1 to promote infection.
in Nature communications
Description | We have uncovered that the antibiotic resistant microbe Klebsiella pneumoniae exploits a protein, KivA, that injects into immune cells to dampen the activation of defences. KivA contains a domain present in receptors of the IL17 signalling pathway, suggesting that Klebsiella has hijacked this domain from our cells for its own benefit. The system that Klebsiella uses to inject KivA is also necessary for killing other bacteria occupying the same niche, although KivA does not have any antimicrobial function. |
Exploitation Route | Pharma companies may develop drugs to target KivA. Notably, there are similar proteins in other pathogens, indicating that the drugs may be useful againts different infections. Drugs targeting KivA will prevent that the pathogens will dampen host antimicrobial pathways, resulting in sustain protective responses. |
Sectors | Healthcare Pharmaceuticals and Medical Biotechnology |
Description | DeF PhD studenship |
Amount | £70,000 (GBP) |
Organisation | Government of Northern Ireland |
Sector | Public |
Country | United Kingdom |
Start | 08/2020 |
End | 03/2024 |
Description | DeF PhD studenship |
Amount | £70,000 (GBP) |
Organisation | Government of Northern Ireland |
Sector | Public |
Country | United Kingdom |
Start | 09/2022 |
End | 09/2026 |
Title | Assay to test bacterial competition |
Description | We have developed a high-throughput method to probe the contact dependent competition between bacterial species. The assay is quantitative and allows probing thousands of bacterial isolates. |
Type Of Material | Technology assay or reagent |
Year Produced | 2023 |
Provided To Others? | No |
Impact | This assay allows to address questions of interest in the context of polymicrobial communities such as the gut. For example, it can help the rational design of consortia able to compete with pathogens, avoiding tissue colonization. |
Title | Method to assess SARS-CoV-2 and bacterial co-infections |
Description | We have developed a method to assess virus and bacteria co-infections challenging a translational relevant human model , PBMCs. The method allows to ass viral and bacterial outcomes, cell activation by mass optometry, and cell transcriptomics (single cell RNA seq, and bulk RNA seq). |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | This method has allowed us to decipher for the first time the effect of SARS-CoV-2 and immune cells resulting in an impairment to clear bacterila infections. This method can be applied to other viral infections. |
Title | Method to assess the interaction between pathogens and immune cells in vivo using mass cytometry |
Description | We have developed a novel method to detect the interaction between Klebsiella pneumoniaer and immune cells in vivo and ex vivo by exploiting mass cytometry. This method allows the simultaneous detection of bacteria, and immune cells characterized with more than 30 markers. |
Type Of Material | Technology assay or reagent |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | This method has allowed to detect interactions between K. pneumoniae and cells never reported before. These findings will allow to investigate how Klebsiella manipulate immune cells, and to better understand how the immune system senses this infection. |
Title | Platform to probe the interaction of pathogens with the innate immune system |
Description | We have developed a platform of high-throughput tests allowing to dissect the effect of bacterial infections on key elements of the innate immune system:(i) intracellular survival in macrophages, (ii) activation of inflammatory pathways (NF-kB and IRF3 in mouse and human macrophages), (iii) activation of inflammasome (IL1b secretion, and pyroptosis). |
Type Of Material | Technology assay or reagent |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | This platform should be instrumental to define signature of infection and correlates of protection for antibiotic resistant infections. |
Description | Invited speaker Biochemical Society Trinity College Dublin |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Policymakers/politicians |
Results and Impact | Invited talk to present our UKRI-funded research on how antibiotic resistant infections counteract the innate immune system. The talk spark collaborations for future research projects. |
Year(s) Of Engagement Activity | 2024 |
Description | Invited speaker Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited to present our UKRI-funded research on how a better understanding of the infection biology of antibiotic resistant infections can be translated to new therapeutics. The talk spark discussions for potential collaborations. |
Year(s) Of Engagement Activity | 2023 |
Description | Invited speaker University of Birmingham by British Society Immunology Midlands |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invitation to present our UKRI-funded research on how antibiotic resistant infections counteract the activation of the immune system. The visit resulted in a number of additional talks with professionals and some potential new collaborations were discussed. |
Year(s) Of Engagement Activity | 2023 |
Description | Invited speaker University of Manchester |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk to present our UKRI-funded research including our translational work exploited host-directed therapeutics against antibiotic resistant infections. The talk spark a new collaboration probing a compound developed by University of Manchester. |
Year(s) Of Engagement Activity | 2023 |
Description | Northern Ireland Science Festival |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | We presented to the general public, including school kids and patients' groups, the global health issue of the AMR pandemic, and how our research is addressing the problem. The presentation was facilitated by on-hands laboratory work. The presentation attracted questions and change the views on the urgency of the AMR problem. |
Year(s) Of Engagement Activity | 2022 |
Description | Northern Ireland Science Festival |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | We presented to the general public, including school kids and patients' groups, the global health issue of the AMR pandemic, and how our research is addressing the problem. The presentation was facilitated by on-hands laboratory work. The presentation attracted questions and change the views on the urgency of the AMR problem. |
Year(s) Of Engagement Activity | 2024 |
Description | Northern Ireland Science Festival COVID19 research |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | More than 4000 viewers watched the videos on Covid19 research posted in YouTube by the Northern Ireland Science Festival. The videos sparked questions and comments, and resulted in additional interactions. |
Year(s) Of Engagement Activity | 2021 |
URL | https://nisciencefestival.com/e21486-spotlight-on-covid-19-research-at-the-wellcome-wolfson-institut... |