Genome-based insights into the evolution of enterococci

Abstract It is now 15 years since the first genome of a free-living organism was sequenced. Since this milestone, a veritable avalanche of genome sequence data has revolutionized many aspects of microbiology. In this review we will discuss recent progress on the genomics of Enterococcus faecalis and E. faecium, which are the two enterococcal species that cause the large majority of enterococcal infections. We will focus on the genome-based analysis of enterococcal diversity and phylogeny. Studies based on comparative genome hybridization showed 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 will 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.