Due to the considerable knowledge accumulated on Escherichia coli as a model organism and to its versatility causing a major public health concern, E. coli will be considered as a paradigm to study microbial adaptation in the medical context. The purpose of our research is to achieve a better understanding of the ecological, evolutionary and molecular parameters allowing the adaptation of natural isolates of the E. coli species to their various lifestyles, especially those involved in the emergence of virulence and antimicrobial resistance and to develop new original therapeutic approaches to fight this pathogen.
Our project focuses on the commensal niche as we have proposed that extraintestinal virulence is a by-product of commensalism and because it plays a major role in the emergence of resistance, and on specific pathologies, i.e. bacteraemia, ventilator-associated pneumonia, neonatal meningitis and haemolytic uremic syndrome. These pathologies have been chosen because of our expertise, their frequency and/or the fact that they are understudied.
Our research is divided in 5 interconnected parts: (i) sampling and storing E. coli diversity, (ii) epidemiology and molecular evolution of adaptation to various niches, (iii) molecular characterisation of the adaptation, (iv) ecology of the emergence of antibiotic resistance and (v) new antimicrobial approaches, including phagotherapy.