Current research topics
The three main subjects of my research concern three different bacterial species: Escherichia coli, Streptococcus pneumoniae and Mycobacterium tuberculosis.
Eco-evolutionary dynamics of Escherichia coli in the human gut
Escherichia coli is a commensal bacteria of the human gut, although it can also become pathogenic when it spreads to the rest of the body, causing for instance urinary tract or blood infections. Changes in the frequencies of the main phylogenetic groups of E. coli have been observed in France and industrialized countries, along with an increase in virulence and antibiotic resistance within the species, making it a major health issue.
My work focuses on understanding the eco-evolutionary dynamics of this bacteria in the host gut and its transmission between hosts. I am especially interested in the variability within the species, in its commensal (transmission, residence) and pathogenic (virulence, pathogenicity) characteristics.
Vaccination against pneumococcal infections as a selection pressure
Invasive pneumococcal infections affecting young children are caused by Streptococcus pneumoniae, which is a bacteria belonging to the infant's nasopharynx microbime. Vaccines developed in response to these infections target certain specific serotypes, whose frequency in the general population is declining. However, the effectiveness of these vaccines is limited by the emergence of other non-targeted serotypes.
In this context, I am interested in the role of vaccines in the dynamics of these different serotypes, in interaction with transmission chains and the use of antibiotics. I am especially aiming at characterising the role of vaccination as a driver of serotype replacement, through the creation of vacant ecological niches.
Spatial distribution of Mycobacterium tuberculosis diversity
Tuberculosis is one of the world's leading causes of infectious mortality, particularly in developing countries, concurrent with high levels of antibiotic resistance. The most recent genotyping methods are making it possible to better understand the phylogenetic structure of Mycobacterium tuberculosis, and to compare it with the structure of host populations.
My research focuses on the dynamics of these host populations (human and animal) in time and space, in order to identify the transmission patterns of the bacteria, understand the spatial distribution of the genetic diversity currently observed and predict its future distribution.
Former reseach topics
Although I'm no longer actively working on it, I was also involved in other research topics, which I continue to be interested in to this day.
Establishment and spread of introduced populations
Introduced populations, intentionally or not, must succeed both in creating self-sufficient colonies and in spreading throughout their new environment. These two objectives can come into conflict, particularly when the number of introduced individuals is low, as the processes of multiplying and dispersing individuals influence each other and interact with the structure of the invaded environment.
My work focused on the role of spatial heterogeneity within the invaded area, in terms of its quality and connectivity, on the establishment and spread of these populations. I was particularly interested in the mechanisms underlying the advance of invasion fronts and their interaction with the environment.
Commercial cattle movements and infection spread
Farm animal diseases raise health and economic issues, aggravated by the intensive use of antibiotics to treat them. Infectious spread not only results from interactions within a herd, but also from the sale and purchase of animals. Those commercial movements create a network, whose structure can be analyzed, and even modified, in order to prevent the spread of infection beyond the herd.
I aimed to assess the effectiveness of logistical measures (linked to the origin, destination and management of animal transport), specifically among bovines, in order to limit the spread of infections on a regional scale, while taking into account the constraints and infectious dynamics at farm level.