PhD Student Position about pathogens and associated resistance genes (Dijon, FRANCE)

University of Burgundy

A PhD opportunity under the supervision of Dr. Ed Topp is available at the University of Burgundy in Dijon, France.
Interested candidates should send an email to for further information.

Description of the project:

Bacteria from the Clostridia group are important members of the human, animal, and environmental microbiota. A characteristic feature of these bacteria is the production of recalcitrant spores that are very persistent once shed from the gut environment. Several clostridia are pathogens of human (eg Clostridium perfringens and Clostridioides difficile) or animal health concern, and they are becoming increasingly and worryingly resistant to antibiotics. Environmental dissemination of these bacteria may be promoted by agricultural practices such as crop irrigation with wastewater effluent (REUSE: use of gray water), a practice that will surely increase in response to climate change. Furthermore, soil amendment with organic wastes of human or animal origin is being promoted as an important element of the circular economy. There is a concern that products harvested from contaminated crop ground may be a route of transmission of these organisms to humans or food-producing animals. The level of crop contamination with these bacteria, how it varies with agricultural practice, their potential transmission to humans or animals, what health risk this might represent, and how best to manage it are largely open questions.  Within this context, the objectives of the project can include: i) determine the prevalence, and characterize strains as well as the associated resistance genes in different compartments of the environment, ii) establish the influence of several biotic and abiotic parameters on environmental persistence of these germs, iii) determine the risks of transfer of resistance genes to other species, iv) determine the risks of transfer of these pathogens and associated resistance genes to the human microbiota through the consumption of foodstuffs.

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