Uncovering the functional role of microbial extracellular vesicles in the emergence of antibiotic resistance – MicroVesi

Antimicrobial resistance (AMR) is a major global health issue and development threat. Profound knowledge of the mechanisms employed by bacteria to defend themselves under antibiotic selective pressure is critical to controlling the rise and spread of resistant bacteria. A key factor in AMR development is the microenvironment that interacts directly with the bacteria and modulates their behavior. When challenged by antibiotics, the bacteria release extracellular vesicles (EVs) in the microenvironment. EVs are tiny lipid enclosures containing biological information, and we hypothesize that their localization at the bacterial surface serves as an antibiotic shield. The uneven spatial distribution and heterogeneous content of EVs across cells, could lead to various levels of protection against antibiotics and the subsequent emergence of tolerant and/or resistant cells. The MicroVesi project will determine the impact of EV distribution and EV content on the cell’s responsiveness to antibiotic drugs, both at the scale of individual cells and entire populations, using the paradigm commensal E. coli and the pathogen V. cholerae as model organisms. These two microorganisms are known to be important reservoirs for the spread of antibiotic resistance. We will use a combination of genetic tools, high-resolution imaging, controlled microfluidic environments that mimic natural ecological niches, and mathematical methods to analyze the bacteria-EV interplay in real-time. The costs/benefits of EV production on bacterial evolvability will be measured in individuals developing both in mono-species and multi-species microcolonies. From these measurements, we will determine whether EVs represent environmental cues shared between bacteria to protect the population as a whole against antibiotic stress. The originality of the MicroVesi project lies in a multi-disciplinary and multi-scale approach that will identify the EV-dependent mechanisms promoting adaptation. Our collection of evolved strains will provide a valuable resource to understand how EVs released in the environment affect the emergence and maintenance of bacterial diversity. The ubiquitous production of EVs by all microorganisms and the recent use of EVs as a drug delivery vehicle, amplify the need for a better understanding of their physiological role in bacterial natural ecologies and position the MicroVesi project in a central spot to combat emerging and persistent infections.