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Population and functional genomics to unravel antibiotic resistance emergence and pathogenesis of Enterococcus faecium

Friday 1 March 2013

Enterococci are ubiquitous in nature and can be found in soil, water, food, animals and humans. In humans enterococci are natural inhabitants of the gastro-intestinal tract and as such belong to the complex community of bacteria that constitutes the microbiota of the large intestine. Apart from being harmless commensals inhabiting the digestive tract enterococci emerged as the second to third most important nosocomial pathogens the last three decades, with Enterococcus faecium being the Enterococcus species that acquired most antibiotic resistance determinants. In this project we aim to use population and functional genomics-based techniques in combination to unravel the evolutionary developments and mechanisms that contributed to the success of E. faecium as nosocomial pathogen.

Our lab sequenced over 70 E. faecium strains providing first insights in the evolutionary trajectories followed by E. faecium to reach ecological enrichment in the GI-tract of hospitalized patients. Extending this population genomics approach will increase our insight in the existence of possible transmission chains between hospital and non-hospital (animal/environment) reservoirs of multi-resistant E. faecium. The availability of genome sequences also facilitated the development of a transposon library in a clinical E. faecium strain. This library is a very powerful tool to determine the genes important in e.g. clinical infections and colonization. For that purpose the library will be grown under different conditions and presence/absence of mutants will be determined using microarray analysis (M-TraM) and next-generation sequencing (Tn-seq).

A second research line involves the investigation of the interaction of E. faecium with components of the innate immune system, cell lines and extracellular matrix molecules. These studies include in vitro as well as in vivo assays, the latter involving experimental infections and colonization models in mice.

Finally, since biofilm formation (BF) (on e.g. intravenous catheters, heart valves, implanted prostheses) is considered to be an important step in the pathogenesis of E. faecium infections we have research program including functional genomics to decipher the different determinants of E. faecium that are implicated in BF formations. This may help to define molecular drug targets to combat BF formation in future. For this, several in vitro assays have been developed to visualize BF with state-of-the-art microscopy (Confocal laser scanning microscopy, Scanning electron microscope, and Transmission electron microscopy).

With this research portfolio, we aim to gain insight into the evolutionary dynamics of E. faecium and the pathophysiology of E. faecium infections.

Molecular biology: i.e. DNA cloning, Conjugation, mutagenesis, PCR including real-time PCR, Sequencing, Southern blotting, Northern blotting; data mining of next-generation sequencing data, hybridizations using micro-array technology, protein purification; flow cytometry; ELISA; gel electrophoreses; Western blotting, adhesion assays to extracellular matrix proteins and cell lines; Confocal laser scanning microscopy, Scanning electron microscope and Transmission Electron Microscopy)

6 or 9 months

Dr. R. Willems, tel. 088 75 576 30, R.Willems@umcutrecht.nl