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The evolutionary epidemiology of commensal bacteria: the case of Escherichia coli from 1980 to 2025

Project description

Improving our understanding of the evolutionary dynamics of pathogens

Understanding the rapid adaptation mechanisms of infectious pathogens is key to designing better management strategies. However, existing models often fail to explain these dynamics as the evolutionary processes causing these changes are largely unknown. The EU-funded EvoComBac project aims to address this challenge of evolutionary biology in the bacterial species Escherichia coli. To that end, it will develop a prospective cohort of 200 longitudinally followed healthy volunteers – the largest of its kind – and collect data to analyse and describe the ecology of Escherichia coli from within-host to population level. Ultimately, the project's work will lead to better predictions of evolutionary dynamics and better management policies for infectious pathogens.

Objective

Understanding the rapid adaptation of infectious pathogens is crucial to design better management policies and anticipate future changes. Yet, existing models often fail to explain these dynamics. I will address this major challenge of evolutionary biology in the bacterial species Escherichia coli. E. coli is a commensal of the human gut and an opportunistic pathogen causing infections responsible for more than a million deaths worldwide per year. E. coli has rapidly evolved over the last four decades. From the 1980s, starting from an almost fully sensitive population, multiple antibiotic resistances have emerged and stabilised at an intermediate frequency. Concomitantly, virulence, the propensity to cause infections, increased. The evolutionary processes causing these changes are largely unknown. To elucidate the drivers of the evolution of commensal E. coli, I will develop a prospective cohort of 200 longitudinally followed healthy volunteers—the largest cohort of its kind. We will analyse these data in the light of an integrative statistical and mathematical framework describing the ecology of E. coli from the within-host to the population level. These models will generate testable predictions on the evolution of genomic variants determining virulence, resistance, and colonisation ability. These predictions will be validated on an exceptional existing dataset composed of 1000 bacterial genomes sampled from healthy human hosts from 1980 to 2025 encompassing around 100,000 generations of bacterial evolution. This original interdisciplinary framework draws from epidemiology, evolutionary biology and genomics for a better understanding of the evolution of bacteria. This project is a step towards better predictions of evolutionary dynamics and better stewardship policies for infectious pathogens.

Host institution

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Net EU contribution
€ 1 070 018,00
Address
RUE MICHEL ANGE 3
75794 Paris
France

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Region
Ile-de-France Ile-de-France Paris
Activity type
Research Organisations
Links
Total cost
€ 1 070 018,00

Beneficiaries (2)