title: Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus.
abstract: The enterococci are Gram-positive lactic acid bacteria that inhabit the gastrointestinal tracts of diverse hosts. However, Enterococcus faecium and E. faecalis have emerged as leading causes of multidrug-resistant hospital-acquired infections. The mechanism by which a well-adapted commensal evolved into a hospital pathogen is poorly understood. In this study, we examined high-quality draft genome data for evidence of key events in the evolution of the leading causes of enterococcal infections, including E. faecalis, E. faecium, E. casseliflavus, and E. gallinarum. We characterized two clades within what is currently classified as E. faecium and identified traits characteristic of each, including variation in operons for cell wall carbohydrate and putative capsule biosynthesis. We examined the extent of recombination between the two E. faecium clades and identified two strains with mosaic genomes. We determined the underlying genetics for the defining characteristics of the motile enterococci E. casseliflavus and E. gallinarum. Further, we identified species-specific traits that could be used to advance the detection of medically relevant enterococci and their identification to the species level.
authors.affiliation: Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Kelli L
authors.initials: KL
authors.lastname: Palmer
authors.forename: Paul
authors.initials: P
authors.lastname: Godfrey
authors.forename: Allison
authors.initials: A
authors.lastname: Griggs
authors.forename: Veronica N
authors.initials: VN
authors.lastname: Kos
authors.forename: Jeremy
authors.initials: J
authors.lastname: Zucker
authors.forename: Christopher
authors.initials: C
authors.lastname: Desjardins
authors.forename: Gustavo
authors.initials: G
authors.lastname: Cerqueira
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Suzanne
authors.initials: S
authors.lastname: Walker
authors.forename: Jennifer
authors.initials: J
authors.lastname: Wortman
authors.forename: Michael
authors.initials: M
authors.lastname: Feldgarden
authors.forename: Brian
authors.initials: B
authors.lastname: Haas
authors.forename: Bruce
authors.initials: B
authors.lastname: Birren
authors.forename: Michael S
authors.initials: MS
authors.lastname: Gilmore
mesh_terms: D000483:Alleles; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002473:Cell Wall / Q000235:genetics / Q000378:metabolism; D016983:Enterococcus / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D019143:Evolution, Molecular; D056426:Genetic Loci; D014644:Genetic Variation; D016680:Genome, Bacterial; D016908:Gram-Positive Bacterial Infections / Q000382:microbiology; D054884:Host-Pathogen Interactions; D010802:Phylogeny; D011135:Polysaccharides, Bacterial / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D011135:Polysaccharides, Bacterial