Genome-based insights into the evolution of enterococci

It is now 15 years since the first genome of a free-living organism was sequenced. Subsequent to this milestone, a veritable avalanche of genome sequence data has revolutionized many aspects of microbiology. In this review, we discuss recent progress on the genomics of Enterococcus faecalis and Enterococcus faecium, which are the two enterococcal species that cause the large majority of enterococcal infections. We focus on the genome-based analysis of enterococcal diversity and phylogeny. Studies based on comparative genome hybridization have shown that both species exhibit considerable inter-strain genomic diversity, which is mainly linked to the variable presence of phages, plasmids, pathogenicity islands and conjugative elements. We also discuss how the advent of next-generation sequencing technologies allows for a comprehensive characterization of the gene repertoire of multiple isolates, which can be used for extremely robust analyses of diversity and population structure.