The gut microbiota of hospitalised patients: insights on Enterococcus faecium

Hundreds of trillions of microorganisms are estimated to live in our gastrointestinal tract and all together we call them the gut microbiota. This microbiota uniquely contributes to the host physiology, including (i) immunomodulation and homeostasis, (ii) colonisation resistance, (iii) metabolization of nutrients, drugs and bile acids. Despite its fundamental role in shaping a state of health and disease in the host, a lot is unknown about the molecular mechanisms and the gut microbiota composition responsible for these activities. The work presented in this thesis aims to describe the role and impact of hospitalization on the gut microbiota composition in critically ill patients and further investigate the concept of dysbiosis in this vulnerable population by focusing on a specific lineage of E. faecium frequently detected in our hospital. As a side effect of long-term hospitalisation, this opportunistic gastrointestinal pathogen has been often identified in high abundance in the gut microbiota of critically ill patients. We intended to unravel the molecular epidemiology and characteristics that account for the successful spread of the hyperendemic lineage ST117/CT24 of E. faecium and propose additional typing methods for rapidly identifying strains in an outbreak scenario.