Fighting Antibiotic Resistance in E. coli with Eligobiotics – FAREWEL

The use of antibiotics has revolutionized modern medicine, increasing our life expectancy and allowing for more complex medical procedures. Antibiotic resistance is becoming a pressing issue, exacerbated by the lack of antibiotic development, with only 5 new molecules in clinical Phases II or III, none of them representing a new class of compound. A second limitation with the use of traditional antibiotics is that they have a broad spectrum of action: many different bacterial species will be killed, including those that are beneficial. The disappearance or reduction of these species can leave free ecological niches that are sometimes colonized by disease-causing, resistant bacterial variants. There is therefore an urgent need for targeted therapies that enable a precise control of complex microbial ecosystems at will, including the reduction of antibiotic-resistant bacteria.
Towards this goal, we developed the first programmable sequence-specific antimicrobials. Our technology relies on a biological vector derived from bacteriophages, called phagemid, which can deliver a therapeutic genetic circuit only to the specific bacteria of choice. We programmed a phagemid particle to deliver a genetic circuit containing CRISPR/Cas9, which encode very specific DNA-sequence targeting and cleavage elements. This approach allows for two control points to be implemented, as opposed to traditional antibiotic molecules: first, we take advantage of the natural capacity of the bacteriophages to recognize only a small subset of bacterial species; second, within those species, only those that contain the targeted DNA sequence will be killed, leaving the rest of the population intact. In this project, we will focus on one of the emergent and more serious threats caused by antibiotic resistant bacteria: we will generate a targeted therapy that will allow for the destruction of Extended-Spectrum Beta-Lactamase E. coli (ESBL-E.coli).
To do this, we will first screen for new natural bacteriophages that can be used as delivery vehicles to target pathogenic bacteria. We are implementing high-throughput robotic technologies to accelerate the discovery process that will allow us to screen for phage variants with different characteristics, such as host range and injection capacities. State-of-the-art sequencing techniques will also help us shed light on the determination of viral DNA packaging elements, which we will then implement into the pipeline of pure, engineered phagemid production. In parallel, we are applying novel bioengineering techniques to modify both previously described phages and newly discovered variants to alter their host cell tropism, synthesize and pack our targeted genetic circuits and include mechanisms to bypass the natural bacterial defenses against phages. Finally, we will establish an ESBL-E.coli mouse colonization model to demonstrate the efficacy of our targeted antimicrobials. This will enable to optimize and quantify the efficiency of delivery and targeted killing of these pathogenic bacteria in a variety of conditions.
In sum, the knowledge and tools which will be developed in this project will open the field of “bacterial gene-therapy”, enabling precise microbiome manipulation and targeted killing within complex microbial ecosystems, and could therefore lead to next-generation personalized therapies. Such a strategy could have impactful applications in human health, notably to control and treat several infectious diseases.