Large-scale differential gene expression in vancomycin-resistant Enterococcus faecium upon interaction with human-derived colonic epithelium

Vancomycin resistant Enterococcus faecium is an opportunistic pathogen that is able to colonize the intestines of hospitalized patients. This initial colonization is an important step in the downstream pathogenesis, which includes outgrowth of the intestinal microbiota and potential subsequent infection of the host. The impact of intestinal overgrowth on host-enterococcal interactions is not well understood. We therefore applied a dual RNA sequencing approach in order to unravel the transcriptional dynamics of both E. faecium and human derived colonic epithelium upon co-culturing. Cultures of colonic epithelium and co-cultures of colonic epithelium and hospital-associated vancomycin resistant (vanA-type) E. faecium were first visualized by confocal microscopy, which revealed that E. faecium resided on top of the colonic epithelium rather than being positioned between colonic cells. RNA sequencing revealed that exposure to the colonic epithelium resulted in the upregulation of E. faecium genes present in plasmid 2, including genes implicated in pili expression and conjugation, and a downregulation of vancomycin resistance genes, besides upregulation of genes related to sugar uptake and biofilm formation. Furthermore, pathway analysis revealed an overall switch in metabolism to amino acid scavenging and reduction. Analysis of the host response upon E. faecium colonization showed a large variation between batches due to the low reads coverage. In summary, our study demonstrates that co-culturing of E. faecium with human colonic epithelium initiates an elaborate gene response in both E. faecium and host cells which enhances our insight in host-E. faecium interactions.