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Daniel Martak thesis defense

Daniel Martak is pleased to invite you to his thesis defence entitled, Epidemiology of Gram-negative bacilli in the community, the environment and food. It will take place on Friday 18 June 2021, at 2pm, in the amphitheatre E019 of the Faculty of Medicine (UFR SMP) of Besançon.

Due to sanitary restrictions, it is necessary to register in advance with Daniel Martak (daniel.martak at
The defense will also be offered by videoconference.
Here is the connection link:

Jury composition
Dr. Marisa Haenni, Anses, Lyon, Rapporteur
Dr. Christophe Merlin, University of Lorraine, Rapporteur
Prof. Anne-Marie Rogues, University of Bordeaux, Examiner
Prof. Christophe Dagot, University of Limoges, Examiner
Prof. Didier Hocquet, University of Bourgogne-Franche-Comté, Thesis Director
Prof. Xavier Bertrand, University of Bourgogne-Franche-Comté, Supervisor

Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa are Gram-negative bacilli frequently responsible for nosocomial infections. Their spread in healthcare systems has been well characterised but the intestinal carriage and transmission dynamics of these pathogens in the community are poorly understood. The One Health concept supports the idea that bacterial populations found in humans, animals and the environment are interconnected. Enterobacteriaceae producing extended-spectrum β-lactamases (EBLSE), responsible for infections associated with high morbidity and mortality, are of particular interest because they widely contaminate food, which could thus be a source of EBLSE for consumers. We used a whole genome sequencing (WGS) approach on a large collection of isolates from residents of long-term care facilities, food and wastewater from five European cities. A first study showed that, in general, food- and sewage-derived EBLSE populations are dissociated and have different antibiotic resistance genes. This suggests that food is not a major source of EBLSE for humans. A second study found that residents of long-term care facilities were very frequent (51.6%) digestive carriers of P. aeruginosa. This carriage was associated with age and obesity and involved a genetically diverse population of P. aeruginosa. Overall, our data show that a complete understanding of the distribution of Gram-negative bacilli and antibiotic resistance genes requires the examination of complete bacterial genomes.

Key words: E. coli, K. pneumoniae, ESBL, CTX-M, food, environment, P. aeruginosa, carriage

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