mARs: Mobile DNA driven antibiotic resistance spreading: molecular strategies, control and evolution for broad distribution

Project Information

mARs

Grant agreement ID: 866250

DOI

10.3030/866250

EC signature date 30 January 2020

Start date 1 July 2021

End date 30 June 2027

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 118,00

EU contribution

€ 1 999 118,00

Coordinated by

UNIVERSITE DE GENEVE
Switzerland

Periodic Reporting for period 3 - mARs (mARs: Mobile DNA driven antibiotic resistance spreading: molecular strategies, control and evolution for broad distribution)

Reporting period: 2024-07-01 to 2025-12-31

Summary of the context and overall objectives of the project

Antibiotic resistance is one of the greatest current global health challenges. Resistance to new antibiotics develops rapidly and the transfer of resistance determinants between bacteria constantly generates more dangerous multidrug-resistant pathogens. Such ‘superbugs’ infect millions of people worldwide, leading to EUR billions of healthcare costs and nearly as many deaths as cancer every year. Mobile genetic elements (MGEs), segments of DNA that can move between bacterial cells, effectively propagate antibiotic resistance in human and natural environments and largely contribute to the emergence of multidrug-resistant pathogens. Yet, our knowledge of their mechanisms is sparse, which hampers the development of new strategies against resistance spreading.
The mARs project uses an multidisciplinary approach combining informatics, genetics, microbiology, and molecular structure analysis to shed light onto MGE-driven resistance transfer in bacteria. It aims to (a) investigate the molecular pathways and regulation of resistance gene movement; (b) dissect the structure of the responsible molecular machineries; and (c) characterize the diversity, evolution and functional success of distinct MGE pathways. Mechanistic work focuses on mobile elements that are highly prevalent in hospitals and confer resistance to critical antibiotics. Bioinformatic quests are then added to chart the global significance of different molecular pathways. By bridging disciplines, we will provide functionally annotated molecular movies of MGE movement and explain how specific molecular strategies evolved to enable broad spreading of resistance determinants.
Upon successful completion, the project will deliver in-depth knowledge on major resistance transfer pathways from atomic to physiological and evolutionary scales, providing a substantial advance in our understanding of the molecular determinants and physiological trends of resistance transmission. Furthermore, the results will have key implications for the development of novel strategies against resistance dissemination in bacteria and can ultimately help to open new frontiers for tackling this major healthcare challenge.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

To date, our studies focused on investigating the molecular pathways of MGE movement and the structures of the underlying molecular machineries. We have bioinformatically surveyed MGEs, identified their conserved parts, and analysed their resistance cargos and transfer trends. Experimental work then characterized essential and accessory components of MGE movement, identified regulatory MGE- and host-derived factors, and reconstituted the biochemical pathways of four MGE families. Analysis of other MGEs is still underway.
We further probed the effect of environmental factors on MGE movement. We tested chemical compounds that were selected in a primary screen for transposition effectors and found that several antibiotics can inhibit MGE mobilization by directly acting on the core protein-DNA complex. A high-throughput assays to further screen MGE cell-to-cell transfer effectors in model bacteria and in the native hosts is currently under active development.
For structural studies, we selected wide-spread MGEs that carry critical drug-resistance genes, and visualized the protein-DNA complexes that move them. Using X-ray crystallography and cryogenic electron microscopy methods, we captured five structures of core MGE proteins or complexes and ten structures of complete regulatory MGE assemblies. These structures visualize key steps of MGE movement and elucidate how complex DNA shapes and intricate biochemical mechanisms enable these elements to move between diverse locations in diverse genomes. The data give unprecedented views of MGE movement and form the basis of four manuscripts that are currently undergoing publication.
With these advances, the project already provided important insights into MGE transfer mechanisms and substantial progress has been made towards discovering and validating their environmental effectors and transfer traits. Current efforts focus on obtaining a global picture of key molecular strategies, dynamic features and regulatory processes that underlie the role of these elements in broad transfer of antibiotic resistance.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Control of bacterial infections is threatened by the rapid emergence of antibiotic resistance, with multidrug-resistant pathogens occurring in alarming numbers worldwide. In the last decades, much research has been devoted to developing new antibiotics, but this has not allowed us to escape the continuous growth of resistance. To tackle this challenge, new strategies that can limit the spread of resistance are needed. However, the development of such interventions is currently hampered by the lack of mechanistic knowledge on resistance transfer pathways.
Research in the mARs project aims to shed light onto fundamental mechanisms of resistance transfer by mobile genetic elements (MGEs) and to improve our understanding on the key molecular determinants and physiological conditions that allow these DNA vehicles to spread broadly in diverse bacteria. The data acquired here will (i) create a complete inventory of all players and reaction intermediates involved in MGE movement, (ii) present high-resolution movies of active molecular machineries and their conformational transitions, and (iii) provide a global view on the mechanistic diversity and evolution of resistance carrying MGEs.
The work will discover basic biological concepts underlying the exchange of genetic material and the adaptation of living organisms to changing environments. Thus, it is expected to deliver important fundamental insights with direct relevance to society and health care. The resulting knowledge may also offer novel solutions to control gene transfer and reduce the spread of antibiotic resistance. Possibilities for translational avenues include (i) improved detection of mobile resistance for better risk assessment (ii) consideration of transfer effectors for optimized treatment strategies, and (iii) development of MGE inhibitors as resistance transfer blockers.

Key objectives and research strategy of the mARs project