Call: Innovations against antibiotic-resistant bacteria: New targets, compounds and tools

6th call, 2018

Fighting antibiotic-resistant superbugs with anti-persister compounds targeting the stringent response (Anti-Persistence)

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Pathogenic antibiotic-resistant “superbugs” are increasing at an alarming pace. Persistence to antibiotics favours the emergence of resistance as mutations increasing antibiotic tolerance favour selection of resistance mutations.

Ongoing project

Persisters constitute subpopulations of cells that can withstand bactericidal antibiotics and are considered as a primary source of infections since they are difficult or impossible to eradicate with conventional antibiotics. Persister bacteria are encountered in a variety of chronic pathologies, including cystic fibrosis, pneumonia and tuberculosis.

Thus the impact of persistence on public health is enormous and there is a pressing need to develop treatments to kill persisters. The existence of a causal link between persisters and persistent infections was demonstrated for S. typhimurium, whose survival inside the host relies on ppGpp. Compounds capable of killing persisters could sterilise S. aureus cultures and cured methicillin-resistant S. aureus (MRSA)infected mice. Thus targeting the enzymes that regulate ppGpp is an interesting and unexplored route to develop new antibiotics active against persisters.

This project aims to target key steps in the mechanism of ppGpp synthesis and hydrolysis in a variety of pathogenic bacteria. In an integrative biochemistry, structural and cellular biology based approach we will uncover novel mechanistic aspects of persistence, deliver novel metabolic biosensors for single-cell analysis and methodologies to study persisters in human pathogens, and discover and validate novel compounds with antipersister action.

Project partners

  • Abel Garcia-Pino, Université Libre de Bruxelles, Belgium (Coordinator)
  • Leonardo Pardo, Universitat Autònoma de Barcelona, Spain
  • Ewa Laskowska, University of Gdansk, Poland
  • Olivier Neyrolles, Université de Toulouse, France

Since the discovery of penicillin by Fleming in the late 1920s, antibiotics have revolutionized the field of medicine and human society in general. However, the antibiotic development pipeline dried out in the late 1980s and we have now reached a critical point where many antibiotics are no longer effective against even the simplest infections. In this context, infectious diseases are now the second leading cause of death in the world with 17 million people dying each year from bacterial infections worldwide.

Pathogenic antibiotic-resistant “superbugs” are a particularly problematic emergent global health threat growing at an alarming pace. These superbugs are typically highly antibiotic tolerant and multi-drug resistant. One of the survival strategies of these pathogens is to enter in a seemingly “dormant” state that suspends cell division known as persister state. Disguised as persisters, bacteria become highly tolerant to antibiotics and stress in general, therefore targeting persisters has become one of the modern challenges of microbiology. These non-growing bacteria are encountered in a variety of chronic pathologies, including cystic fibrosis, pneumonia and tuberculosis (TB).

Thus the impact of persistence on public health is thus enormous and there is a pressing need to develop treatments to kill persisters. It has been previously shown that a strategy that addresses the persistence problem is a promising approach in the fight against multi-drug resistant superbugs. Therefore this project aims to target key steps in the mechanisms of pathogenic bacteria to regulate stress that are involved in persistence from integrative biochemistry-, structural and cellular biology-based perspective to discover novel compounds that could lead to the development of new types of antibiotics.

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Design, synthesis and lead generation of novel siderophore conjugates for the detection and treatment of infections by Gram-negative pathogens (SCAN)

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There is a strong need for novel, innovative therapeutic solutions for infections caused by Gramnegative pathogens. In addition, there is a lack of tools to diagnose bacterial infections at deep body sites, e.g. on implant surfaces.

Ongoing project

In the project SCAN (Siderophore Conjugates Against Gram-Negatives), we apply a rational design approach to establish a targeting conjugate platform that can be used to both diagnose as well as treat bacterial infections (‘theranostics’ principle). The conjugates are actively transported into bacteria through their iron transport machinery that accepts siderophores as substrates.

This concept has recently been validated clinically and addresses a key issue of Gramnegative pathogens, the impaired translocation into the cell. We will design and synthesise novel siderophores that employ novel central scaffolds and combinations of iron-binding motifs. Those will be coupled with hitherto unexplored effectors: RNA polymerase inhibitors are employed as potent antibiotics, and dioxetane-based chemiluminescent probes will be used for imaging.

As a linkage between siderophore and antibiotic, cleavable, self-immolative linkers (e.g. trimethyl lock) will be constructed. The conjugates will be characterised in cellular assays and in infection models in mice. Their translocation and resistance mechanisms will be investigated by genetic and proteomic methods. The project should yield novel antibiotic lead structures with proven efficacy in vivo.

Project partners

  • Mark Brönstrup, Helmholtz Centre for Infection Research, Germany (Coordinator)
  • Doron Shabat, Tel-Aviv University, Israel
  • Isabelle Schalk, CNRS – Université de Strasbourg, France

Infections caused by multidrug-resistant Gram-negative bacteria result in significant mortality and morbidity worldwide. In line with this, all pathogens that received a ‘critical’ status by the recently established WHO priority list were drug-resistant Gram-negative species. The reasons for limited success of pharmaceutical research programs in the area of antibiotics have been carefully analyzed: the main hurdle is the limited understanding how to get drugs into Gram-negative bacteria. Thus, there is a strong need for novel, innovative drugs against infections caused by Gram-negative pathogens. There is also a lack of tools to diagnose bacterial infections at deep body sites, e.g. on implant surfaces.

In the project SCAN (Siderophore Conjugates Against gram-Negatives), we apply a rational design approach to establish a targeting conjugate platform that can be used to both diagnose and treat bacterial infections (‘theranostics’ principle). The conjugates are actively transported into bacteria through their iron transport machinery that accepts siderophores as substrates. As this resembles the strategy of ancient Trojan warriors, the approach has been named the ‘Trojan Horse Strategy’. This concept has recently been validated clinically, a first drug (Fetroja) has been approved and is available to patients.

We will design and synthesize artificial siderophores that employ novel central scaffolds and combinations of iron-binding motifs. Those will be coupled with hitherto unexplored effectors: RNA polymerase inhibitors are employed as potent antibiotics, and chemiluminescent probes will be used for imaging. As a linkage between siderophore and antibiotic, cleavable, self-immolative linkers will be constructed. The conjugates will be characterized in cellular assays and in animal infection models. Their translocation and resistance mechanisms will be investigated by genetic and proteomic methods.

The project should yield novel antibiotic lead structures as well as activatable bacterial probes with proven efficacy in vivo to detect and treat infections. Taken together, the afforded antimicrobials and moreover the novel theranostics could be tools that allow for strain-specific, potent treatment and monitoring of bacterial infections, addressing a major medical need expressed by the WHO.

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Development of novel ribosome-targeting antibiotics (RIBOTARGET)

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The ribosome is one of the major targets for antibiotics. Multi-drug resistant pathogens are making our current arsenal of ribosome-targeting antibiotics obsolete, highlighting the need for development of new antimicrobial compounds.

Ongoing project

Here we focus on discovering novel ribosometargeting antibiotics with improved activity and selectivity, with chemical scaffolds that target novel sites on the ribosome and different steps of the translation cycle.

Specifically, we propose to (WP1) develop novel aminoglycoside antibiotics with potent antibacterial activity and improved target selectivity to overcome the toxicity that is associated with this clinically important class of antibiotics; (WP2) develop proline-rich antimicrobial peptides as novel antimicrobial agents by taking advantage of available high resolution ribosome structures and their ease of synthesis and modification; (WP34) utilise high-throughput screening to discover compounds with novel chemical scaffolds that have activity against new cellular targets, such as the (WP3) ribosome rescue systems, and (WP4) stringent response pathways in bacteria.

The consortium aims to characterise the mechanism of action of novel antimicrobial agents as well as their in vivo and in vitro efficacy, in particular against Priority 1 pathogens and Mycobacterium tuberculosis.

Project partners

  • Daniel Wilson, University of Hamburg, Germany (Coordinator)
  • C. Axel Innis, Institut Européen de Chimie et Biologie, France
  • Erik Böttger, University of Zurich, Switzerland
  • Vasili Hauryliuk, Umeå University, Sweden
  • Reynald Gillet, Université de Rennes, France
  • Dominik Rejman, The Czech Academy of Sciences, Czech Republic
  • Marco Scocchi, University of Trieste, Italy

Multi-drug resistant pathogens are making our current arsenal of ribosome-targeting antibiotics obsolete, highlighting the need for development of new antimicrobial compounds.

The RIBOTARGET consortium aims to discover novel ribosome-targeting antibiotics with improved activity and selectivity against Priority 1 pathogens and Mycobacterium tuberculosis, with chemical scaffolds that target novel sites on the ribosome and different steps of the translation cycle. This includes development of (i) novel aminoglycoside antibiotics with potent antibacterial activity and improved target selectivity to overcome the toxicity that is associated with this clinically important class of antibiotics; (ii) proline-rich antimicrobial peptides as novel antimicrobial agents by taking advantage of available high resolution ribosome structures and their ease of synthesis and modification, as well as (iii-iv) utilizing high-throughput screening to discover compounds with novel chemical scaffolds that have activity against new cellular targets, such as the (iii) ribosome rescue systems, and (iv) stringent response pathways in bacteria.

To achieve these aims our multi-interdisciplinary RIBOTARGET consortium brings together leading scientists with complementary expertise in microbiology, biochemistry, chemical synthesis and structural biology. This will enable us to characterize the mechanism of action of novel antimicrobial agents as well as their in vivo and in vitro efficacy.

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Restoring E. coli Sensitivity for Antibiotics by blocking TolC-Mediated Efflux (RESET-ME)

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Overexpression of efflux pumps is a major factor for drug resistance in Gram-negative bacteria. In E. coli, the AcrAB-TolC efflux pump complex transports antibiotics from the periplasm or cytoplasm into the external medium. As TolC deletion has been shown to result in increased susceptibilities of E. coli to several antibiotics, it may represent an attractive drug target.

Ongoing project

Recently, we have identified the first organic small molecule that effectively blocks TolC function using virtual screening in combination with experimental validation of the in silico hits by surface plasmon resonance (SPR) and electrophysiology studies. Building on these results, we propose to further develop this compound and in parallel to identify and develop novel TolC blockers within an interdisciplinary consortium.

The already known blocker will be progressed in three rounds of optimisation. Each round comprises compound modifications by medicinal chemistry, assessment of TolC binding and blockage using SPR and electrophysiology, various antimicrobial studies and ADMETox profiling. Novel small molecules blocking TolC will be identified and optimised using the same experimental platform, starting with virtual screening for identification of novel compounds targeting TolC. Experimentally validated TolC blockers will be progressed in two rounds of optimisation. Ultimately, this approach will allow to assess TolC target validity for adjuvants in antimicrobial therapies and result in potent TolC blockers that may be further developed into drugs restoring E. coli susceptibility to antibiotics.

Project partners

  • Björn Windshügel, Fraunhofer Institute for Molecular Biology and Applied Ecology, IME, Germany (Coordinator)
  • Mathias Winterhalter, Jacobs University Bremen, Germany
  • Päivi Tammela, University of Helsinki, Finland
  • Aigars Jirgensons, Latvian Institute of Organic Synthesis, Latvia
  • Matteo Ceccarelli, University of Cagliari, Italy

Bacteria have developed several resistance mechanisms against antibiotics. One of these mechanisms involves fast removal of antibiotics from the bacterium. This results in an impaired effect of antibiotics. For this purpose, bacteria use so-called efflux pumps, which are large protein complexes composed of three different components. In E. coli, this complex consists of a pump located in the inner membrane (AcrB),a periplasmic adapter protein (AcrA)and the outer membrane factor TolC.

The aim of our project is to develop molecules that block the outer membrane factor TolCin a way that antibiotics cannot be removed anymore from the bacterium. As a consequence, the efficacy of antibiotics can be improved significantly. In this project, an interdisciplinary team composed of research groups from Germany, Finland, Latvia, and Italy combines different experimental and computational techniques for identification and optimization of efflux pump blockers which sensitize E. colibacteria for antibiotics. If successful, the approach will be applied also to other human pathogenic bacteria.

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Development of novel Mycobacterial Tolerance Inhibitors (MTIs) against MDR/XDR tuberculosis (MTI4MDR-TB)

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In 2017, WHO published the Global Priority Pathogen lists with the aim to promote research and development of new treatments that are effective against microbes resistant to multiple antibiotics. Among them, multi- and extensively drug resistant Mycobacterium tuberculosis caused 48% of new tuberculosis (TB) cases in some countries in 2016.

Ongoing project

Current regimens for the treatment of TB include a combination of antibiotics developed for their strong efficacy against drug sensitive bacterium. The inadequacies of present TB therapies demand discovery of new agents with unique mechanisms of action to treat Mtb infection. Towards this end, we have discovered and developed a new family of ring-fused 2-pyridones (termed Mycobacterial Tolerance Inhibitors, MTIs) that potently sensitise Mtb to stresses encountered during infection and restores activity to the frontline antibiotic isoniazid (INH) in otherwise INH-resistant Mtb isolates.

Our short-term objectives are to demonstrate preclinical proof-of-concept for MTIs to combat Mtb infection, optimise the current lead MTIs for translation to a therapeutic, and reveal new insights into pathways of drug tolerance and resistance. Our long-term objective is to develop a new orally available antibiotic that improves the current regimens for patients with drug-resistant TB. We will also generate a deeper understanding of the MTI’s mode of action and their potential in synergistic interactions with other drugs. Importantly, we will also study how likely it will be for Mtb to develop resistance to combinations of MTIs and INH and other antibiotics.

Project partners

  • Fredrik Almqvist, Umeå University, Sweden (Coordinator)
  • Camille Locht, University of Lille, CNRS, Inserm, France
  • Tone Tønjum, University of Oslo, Norway
  • Jesús Blázquez, National Center for Biotechnology, CSIC, Spain
  • Christina Stallings, Washington University School of Medicine, USA

In 2017, WHO published the Global Priority Pathogen lists with the aim to promote research and development of new treatments that are effective against microbes resistant to multiple antibiotics. Among them, multi- and extensively drug resistant Mycobacterium tuberculosis caused 48% of new tuberculosis (TB) cases in some countries in 2016. Current regimens for the treatment of TB include a combination of antibiotics developed for their strong efficacy against drug sensitive bacterium. The inadequacies of present TB therapies demand discovery of new agents with unique mechanisms of action to treat Mtb infection. Towards this end, we have discovered and developed a new family of ring-fused 2-pyridones (termed Mycobacterial Tolerance Inhibitors, MTIs) that potently sensitise Mtb to stresses encountered during infection and restores activity to the frontline antibiotic isoniazid (INH) in otherwise INH-resistant Mtb isolates.

Our short-term objectives are to demonstrate preclinical proof-of-concept for MTIs to combat Mtb infection, optimise the current lead MTIs for translation to a therapeutic and reveal new insights into pathways of drug tolerance and resistance. Our long-term objective is to develop a new orally available antibiotic that improves the current regimens for patients with drug-resistant TB. We will also generate a deeper understanding of the MTI’s mode of action and their potential in synergistic interactions with other drugs. Importantly, we will also study how likely it will be for Mtb to develop resistance to combinations of MTIs and INH and other antibiotics.

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Flavodoxin inhibitors to kill resistant bacteria (FLAV4AMR)

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This transnational collaboration gathers the expertise and resources required to address lead improvement to the point of producing novel antibiotics ready for clinical trials, and to clarify the overall importance of flavodoxin as a novel drug target.

Ongoing project

The project has two goals:

  1. To culminate the improvement of inhibitors of the flavodoxin from H. pylori, which have shown efficacy against reference and clinical strains (including a clarithromycin-resistant one) and in a mice model.
  2. To determine the relevance of flavodoxin as a novel drug target to fight bacteria which pose problems associated to antimicrobial resistance.

Project partners

  • Javier Sancho, Javier Sancho, Spain (Coordinator)
  • Eliette Touati, Pasteur Institute, France
  • Ultrich E Schaible, Research Center Borstel, Germany
  • Alain Bousquet-Melou, Ecole Nationale Vétérinaire de Toulouse, France

Some bacteria and other microorganisms are pathogens responsible for human infectious diseases. Bacterial infections are commonly fought using antibiotics or, more generally, antimicrobials. the prolonged use (and misuse) of antimicrobials over time to fight human infections has allowed some bacteria to develop molecular mechanism that neutralize antimicrobials. Such bacteria are in practice antimicrobial resistant and constitute a serious global threat to human health. In the European Union, antimicrobial resistance is responsible for 33,000 deaths annually and the costs of medical care and productivity losses are estimated in 1.5 billion euros.

The bacteria Helicobacter pylori (Hp) has been identified by the WHO as one of the pathogens for which it is urgent to find new antibacterial compounds, due to the high incidence of antibiotic-resistant strains along with the fact that half of the world’s population suffers from gastric infections caused by Hp, and because Hp infection constitutes a risk factor for developing gastric cancer. The Spanish-Franco-German project Flavodoxin inhibitors to kill resistant bacteria (FLAV4AMR), has been conceived as a transnational collaboration that brings together all expertise and resources needed to develop new antimicrobial compounds that could enter clinical testing and renew our arsenal against Hp. These novel antimicrobials act by a mechanism different from those of existing broad-range antimicrobials and therefore may be specific against Hp. Moreover they may not damage the beneficial microbiota and thus be useful for a personalize treatment of infectious diseases.

The project is led by Javier Sancho (Biochemistry Professor, and researcher at the University Institute for Research on Biocomputing and Physics of Complex Systems – BIFI). “Our ultimate goal is to develop new flavodoxin inhibitors having significant antimicrobial activity, both for Hp and for other pathogens that present significant problems because of their antibiotic resistance, and that can reach the market within a reasonable time, then, having a high impact on medicine,”

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Exploration of the TPP riboswitch as a new target for antibiotics (Explore)

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In this project, we will explore the TPP riboswitch as a new drug target for antibiotics for key ESKAPE pathogens (E. coli, K. pneumoniae, A. baumannii, P. aeruginosa, S. aureus) and Streptococcus pneumoniae.

Ongoing project

The TPP riboswitch has already been validated as a drug target, however, potent and drug-like ligands with antibiotic activity are needed as starting points to develop novel strategies for anti-infective treatments. The goal of this proposal is to deliver such compounds. Using an innovative assay technology, we will develop a high-throughput assay that monitors simultaneously transcription efficiency and the regulatory activity of the riboswitch, which is crucial for its action, and use this assay to screen the CZ- and EU-OPENSCREEN libraries of lead-like compounds. The hits obtained will be thoroughly validated and the most promising hits will be optimised to improve their affinity.

The advanced compounds will be evaluated for antibiotic activity against the key ESKAPE pathogens and Streptococcus pneumoniae. We will also assess the broad-spectrum potential of the compounds and carry out mode of action studies to ensure that the compounds act on target. If the TPP riboswitch holds up to its high promises, this project will pave the way for urgently needed new antibiotics.

Project partners

  • Ruth Brenk, University of Bergen, Norway (Coordinator)
  • Petr Bartunek, Institute of Molecular Genetics of the ASCR, Czech Republic
  • Matthias Mack, Mannheim University of Applied Sciences, Germany
  • Gints Smits, Latvian Institute of Organic Synthesis, Latvia
  • Daniel Lafontaine, Université de Sherbrooke, Canada

The antibiotics we are currently using are losing effectiveness due to the emergence of resistant bacteria. Therefore, there is an urgent need to develop new antibiotics. In this project, we aim to develop ligands for an RNA element (a so-called riboswitch), that controls the expression of essential bacterial genes. These ligands can then serve as starting points for drug discovery for future antibiotics.

To reach this goal, we have assembled a team of highly skilled researchers from Norway, the Czech Republic, Latvia, Germany, and Canada. Together, we are developing a test system so that we can screen thousands of molecules for binding to the target. Subsequently, the identified ligands will be optimized to increase their affinity. The advanced compounds will be evaluated for antibiotic activity against the key bacteria for which new antibiotics are urgently needed. We will also carry out mode-of-action-studies to ensure that the compounds act on target as intended. If investigated riboswitch holds up to its high promises, this project will pave the way for urgently needed new antibiotics.

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Fighting antimicrobial resistant infections by high-throughput discovery of biofilm-disrupting agents and mechanisms (DISRUPT)

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Many bacterial infections are associated with biofilms. Biofilm-related infections, particularly those caused by drug resistant bacteria, are difficult to handle with current antibiotic strategies. These includes wound-infections (e.g. caused by Pseudomonas aeruginosa or Staphylococcus aureus), urinary tract infections (e.g. Escherichia coli), chronic airway infections (e.g. P. aeruginosa) and preinfection colonisation by Streptococcus pneumoniae.

Ongoing project

New strategies and compounds to fight such resilient infections are imperative; however, the full repertoire of genes and processes that are essential for biofilm formation in different microbes is unknown. In this project, we aim to provide new tools, targets and agents for understanding and treating biofilm-associated infections in four major AMR pathogens (P. aeruginosa, UPEC, S. aureus and S. pneumoniae). To achieve this, we have assembled an interdisciplinary team with diverse expertise in microbial genetics and genomics, highthroughput screening and antibiotics/antibody research.

Our project involves a combination of stateof-the-art genetic approaches to construct genome-wide tools with automated biofilm-phenotyping and high-throughput screening for anti-biofilm antibodies and chemicals. Finally, we will characterise the mechanism of action of novel anti-biofilm agents.

Project partners

  • Morten Kjos, Norwegian University of Life Sciences, Norway (Coordinator)
  • Jan-Willem Veening, University of Lausanne, Switzerland
  • Athanasios Typas, European Molecular Biology Laboratory , Germany
  • Christoph Merten, European Molecular Biology Laboratory , Germany

Antimicrobial resistance is a growing problem worldwide. Many bacterial infections are nowadays often difficult to treat due to increasing antimicrobial resistance. Infections are particularly problematic if they are associated with biofilms. Biofilms are structured communities of bacteria, which are attached to surfaces. Infections typically caused by biofilms are wound-infections and urinary tract infections. The surface-attached biofilms are held together by a slimy matrix of polysaccharides, lipids, DNA and proteins. The matrix protects the bacterial cells against antibiotics and adds to the already existing resistance, making the infection treatment highly problematic. Novel strategies to treat such infections are therefore critical.

In our project we focus on four bacteria which has been listed as high-priority pathogens by WHO. These are (1) uropathogenic E. coli (the major cause of urinary tract infections and catheher infections), (2) Pseudomonas aeruginosa (whose biofilms are associated with chronic infections in wounds or during cystic fibrosis), (3) Staphylococcus aureus (causing biofilm-associated chronic wound – and medical implant infections), and (4) Streptococcus pneumoniae (whose biofilms have been associated with middle-ear infections and pneumoniae).

The DISRUPT project aims to identify new strategies to treat biofilm-associated infections. By inhibiting bacterial biofilms, the chances of infections will be reduced, and this will also resensitize the bacteria to existing antibiotics. To do this, we are using state-of-the-art genetic technologies (transposon sequencing, CRISPR interference) combined with high-throughput screens (screen for chemicals and microfluidic antibody screens) to identify anti-biofilm agents and mechanisms. The methods and resources we develop will be available for researchers worldwide, and will positively impact a range of research project related to AMR pathogens.

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Advancing CRISPR antimicrobials to combat the bacterial pathogen Klebsiella pneumoniae (CRISPRattacK)

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The increasing incidence of multidrug-resistant bacterial infections and the trickling pipeline of novel antibiotic classes demand a new generation of antimicrobials. One promising avenue has been the development of antimicrobials based on CRISPR-Cas immune systems.

Ongoing project

These systems can be programmed to specifically and efficiently eliminate cells harbouring multi-drug resistance genes without impinging on resident microbiota. However, CRISPR antimicrobials remain to be advanced from a few proof-of-principle demonstrations to established therapeutics that can effectively combat the most pressing pathogens. Here, we propose to advance this antimicrobial platform to selectively kill Klebsiella pneumoniae, a major cause of multi-drug resistant, nosocomial infections worldwide.

We have devised a series of experimental approaches that will identify the most active CRISPR nucleases and DNA target sites for programmed killing, engineer bacteriophage delivery vehicles that can efficiently deliver CRISPR to a large fraction of clinical isolates, and evaluate the efficacy of the most promising therapeutic candidates in mouse infection models. Once demonstrated, the resulting optimised CRISPR antimicrobials will represent a large leap forward for the development of novel antimicrobials against Klebsiella, and they will provide a framework to develop similar antimicrobials against other high-priority pathogens associated with multidrug resistance.

Project partners

  • Chase Beisel, Helmholtz Centre for Infection Research, Germany (Coordinator)
  • Udi Qimron, Tel-Aviv University, Israel
  • David Bikard, Pasteur Institute, France
  • Sylvain Brisse, Pasteur Institute, France
  • Strowig Till, Helmholtz Centre for Infection Research, Germany

Multidrug-resistant bacterial infections are increasingly common, and the trickling pipeline of new antibiotics can do little to stem the tide. Instead, entirely new types of antibiotics are needed. One promising avenue involves CRISPR. CRISPR is best known for genome editing and a means to reverse genetic diseases. However, this same tool also be used to eliminate multidrug resistant pathogens while sparing commensal bacteria inhabiting our bodies. Early work highlighted the promise of these CRISPR antimicrobials, yet it remains a fledgling technology that requires further development before being ready for the clinic.

Through funding from JPIAMR, we are developing CRISPR antimicrobials against Klebsiella pneumoniae, a major cause of multidrug resistant infections worldwide. These pathogens often spread in hospitals and can be resistant to virtually every antibiotic at our disposal. Our goals are to deliver CRISPR to these bacteria using bacterial viruses called bacteriophages and ensure CRISPR can eliminate cells carrying antibiotic resistance. Toward this goal, we have assembled a team of experts in CRISPR biology and technologies, bacteriophage engineering, and Klebsiella. The team has been engineering bacteriophages as vehicles to deliver the CRISPR cargo to different Klebsiella strains found in hospitals. We have also been identifying the best CRISPR enzymes that eradicate cells with target sequences.

Finally, we are working toward experiments in mice that will lay a path toward clinical trials. The resulting optimized CRISPR antimicrobials will represent a leap forward toward the commercial development of novel antimicrobials against Klebsiella, and they will allow us to develop similar CRISPR antimicrobials against other multi-drug resistant pathogens. Through these efforts, we aim to provide new weapons against bacterial infections and turn the tide of antibiotic resistance.

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Anti-biofilm therapies using local application of bacteriophages (ANTIBIO-LAB)

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The use of medical devices has had an enormously positive impact on patient care. However, approximately 5% of patients across all medical specialities can develop an infection associated with the device, which can have disastrous consequences.

Ongoing project

These bacterial infections involve biofilm formation and are therefore always highly antibiotic tolerant, even in the absence of specific antibiotic resistance genes. The antibiotic recalcitrance of the biofilm leads to poor treatment success rates and often requires implant removal to treat the infection.

The ANTIBIO-LAB consortium’s overall aim is to introduce a new concept in the treatment of antibiotic resistant biofilm infections by delivering biofilmadapted bacteriophages in a customised local delivery vehicle. The methods that we will employ draw from our collective experience in phage isolation, phage in vitro evolution, local delivery vehicle design, and clinically relevant in vitro and in vivo models of biofilm infection.

Project partners

  • Fintan Moriarty, AO Research Institute Davos, Switzerland (Coordinator)
  • Andrej Trampuz, Universitätsmedizin Berlin, Germany
  • Willem-Jan Metsemakers, University Hospitals Leuven, Belgium
  • David Eglin, AO Research Institute Davos, Switzerland
  • Rob Lavigne, Université Catholique de Louvain, Belgium
  • Mariagrazia Di Luca, PRO-IMPLANT Foundation, Germany

The use of medical implants has brought about an enormous progress in the care of patients. However, the development of bacterial biofilms adhered on the implant surface and the resulting resistance to antibiotics can lead to repeated infections. These infections lead to poor treatment success in all medical fields and very often, the implant has to be replaced. This project introduces a new concept for the treatment of antibiotic-resistant biofilm infections.

Content and goals of the research project: Bacteriophages are viruses that infect specifically bacterial cells and kill them within minutes to hours. Since bacteriophages require living bacteria to multiply, they cannot reproduce once the infection is eliminated. Therefore, bacteriophages are suitable for the natural and specific therapy of multi-antibiotic-resistant biofilm infections. The main goal of the project is to develop a suitable material for local administration of bacteriophages, which can be used for the treatment of antibiotic-resistant biofilm infections. Different methods and experiments for bacteriophage isolation and adaptation, as well as development of local administration materials and clinically relevant infection models are applied in this project.

Scientific and social context of the research project: The complementarity of the project partners offers a broad knowledge of essential clinical, microbiological and process technology. The project partners have already shown that bacteriophage therapy is an effective anti-infective therapy in the laboratory as well as in patients. Through the collaboration of all project partners, the effectiveness of bacteriophage therapy will be further enhanced by using the latest technologies in local administration materials. An effective therapy would have an enormous impact on the patient.

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