Defense systems limit the infection of bacteria not only by phages, but also more generally by mobile genetic elements, such as plasmids. Bacterial genomes carry on average 5 defense systems, but the number and composition of systems is highly variable from one genome to another, even between genomes that are otherwise very similar. Our current projects aim to better understand how defensomes impact phage-bacteria interactions, how their activity is regulated by the environment, and the selective pressures that drive their composition.
Another important line of research in our group aims to better understand how phages co-infecting the same host population interact with each other, and how these interactions influence the eco-evolutionary dynamics of phages and bacteria.
Role of mobile genetic elements in the propagation of antiviral resistance
Mobile genetic elements (MGE), which are present in most bacteria, often carry adaptive genes (e.g., antimicrobial resistance, virulence) and are key players of horizontal gene transfer. They include phages, conjugative elements, their satellites and mobilizable elements. Recent studies have revealed that defense systems are in fact very often carried by MGE themselves, suggesting that defense systems are primarily involved MGE-MGE competition rather than in bacterial-MGE conflict. In particular, conjugative plasmids and prophages frequently carry defense systems and therefore, they could be key players in the propagation of resistance mechanisms against MGE, and particularly against virulent phages.
Using Pseudomonas aeruginosa as a model we aim to quantify the spread of defensive prophages within the bacterial population, in the presence or absence of virulent phages, and determine how this spread varies with the type of underlying defense mechanism (which may be associated with variable fitness costs) and with various ecological and environmental parameters. We will also look at the tripartite coevolution between virulent phage – prophage – bacterium and characterize the evolved players through phenotypic and genomic analyses.
Using similar approaches, we will study in Escherichia coli the role of conjugative plasmids in the propagation of phage resistance, and reciprocally, measure the impact of phages on plasmid dissemination. The selective pressure imposed by phages may promote the spread of defensive plasmids and we will investigate the mechanistic and ecological conditions that favor this outcome, from the cellular scale to the population level.
Phage community ecology and evolution
Recent metagenomic data suggest that phages frequently share common hosts, providing them with the opportunity to interact with each other. Few mechanisms of direct phage-phage interactions, such as superinfection exclusion, have been studied in details. Phages can also interact indirectly if they consume different shares of the same host population, or via the induction of bacterial immune responses that might be more detrimental to one phage compared to the others. These interactions may have different and unequal effects on the epidemiology of each interacting phage, but their mechanisms and consequences have been very poorly studied. Through the implementation of a systematic approach in E. coli, where we will measure the relative abundances of 2 phages during pairwise competition, we will seek to answer the following questions:
Are interactions mutualistic or antagonistic? What are the genetic and mechanistic bases for either type of interaction? Can they be predicted based on the knowledge of phage genomes? What are their consequences for the ecology and evolution of phage populations?
Determinants of phage host range
The recognition of specific structures at the surface of the cell (e.g., protein, LPS, capsule) is the first step that determines the susceptibility of a bacterium to a phage. Once the phage had adsorbed to its target bacterium and ejected its genome, intracellular defense systems constitute the second determinant of phage susceptibility. Which of surface structures or defense systems is the main determinant of phage susceptibility? Answering this is critical to better understand phage host range. Recent work addressing this question have reported opposite conclusions. Exploring this, we have measured infectivity and adsorption of 9 phages on 125 diverse clinical isolates of P. aeruginosa. Throughgenomic and statistical analyses (e.g., GWAS), we seek to identify genetic elements that correlate with phage susceptibility.
In a parallel study, we used a direct genetic approach to investigate similar questions: systematic deletion of all predicted defense systems in a clinical isolate of E. coli did not broaden the range of phages infecting the strain, suggesting that adsorption factors are better predictors of phage susceptibility.
In summary, we use multidisciplinary approaches from genomics, microbial ecology, evolutionary biology and genetics to investigate phage-host, phage-phage and phage-plasmid interactions from the cellular to population scale.
Our research will provide functional insights on the mechanisms, ecology and evolution of phage resistance in the pathogens Escherichia coli and Pseudomonas aeruginosa and help to better understand the dynamics of natural phage populations. Our results will be important for the development of phage therapy, a promising alternative to antibiotics but which faces the same threat of rapidly spreading resistance.
