Enterococcal genomics is a rapidly growing area of study. The first enterococcal genome sequence—that of Enterococcus faecalis V583—was published ten years ago (McShan & Shankar, 2002; Paulsen, et al., 2003), and complete or draft genome sequences of various enterococcal strains and species now number in the hundreds (http://www.ncbi.nlm.nih.gov/genome). Concurrent with rapid advances in genome sequencing, the sequencing-based classification scheme of multilocus sequence typing (MLST) has been used to interrogate population structures of the two enterococcal species that are most associated with human health and disease, E. faecalis and Enterococcus faecium. These two species also constitute the bulk of enterococcal genome sequence data that has been generated to date. This wealth of genomic data has allowed for an investigation of enterococcal diversity at a depth not previously achievable. Genomic studies in enterococci have been driven by overarching questions, such as: Why do multiple species of enterococci exist that inhabit seemingly identical niches, such as E. faecalis and E. faecium in the human gut, and what ecological factors have contributed to their divergence from a common ancestor? Within an enterococcal species such as E. faecalis or E. faecium, what qualities distinguish one strain from another? Are infection- or hospital-derived strains evolutionarily distinct from strains that benignly co-exist in the complex microbial consortium of the healthy human intestine? Related to this, have antibiotic use and the nosocomial environment led to changes in the enterococcal genome and/or its population structure?
This chapter highlights major advances in enterococcal genomics, including the development of MLST schemes to study the population structures of E. faecalis and E. faecium; comparative genome hybridization (CGH) studies to catalog the genomic contents of hundreds of E. faecalis and E. faecium strains; and significant findings from genome sequencing of multiple enterococcal species, beginning with the discovery and sequencing of the E. faecalis pathogenicity island (PAI). Additionally, we review the use of genome resequencing as a tool to study the short-term evolution of E. faecalis and the use of metagenomics to assemble in situ enterococcal genomes. In concluding the chapter, we discuss future perspectives in enterococcal genomics, including pressing questions that should drive future research in this field. While comparative genomics in enterococci has rapidly advanced over the last ten years, the number of genomes discussed here pales in comparison to what has been emerging—136 enterococcal genomes have been sequenced as part of the Human Microbiome Project (http://www.hmpdacc.org/), and 406 more were sequenced in a large-scale enterococcal genome sequencing endeavor performed in a multi-national collaboration with the Broad Institute (Cambridge, MA). Clearly, our foray into enterococcal genomics has only just begun.