High-Quality Draft Genome Sequences of 28 Enterococcus sp. Isolates

Abstract

The enterococci are low-GC Gram-positive bacteria that have emerged as leading causes of hospital-acquired infection. They are also commensals of the gastrointestinal tract of healthy humans and most other animals with gastrointestinal flora and are important for food fermentations. Here we report the availability of draft genome sequences for 28 enterococcal strains of diverse origin, including the species Enterococcus faecalis, E. faecium, E. casseliflavus, and E. gallinarum.The enterococci are ecologically diverse, Gram-positive lactic acid bacteria that are found in the gastrointestinal consortia of humans, other mammals, reptiles, amphibians, birds, and insects and are utilized in production of fermented foods and probiotics (1, 2, 16). However, they have also emerged as leading causes of hospital-acquired infection at extraintestinal sites, including the heart, urinary tract, and surgical site wounds (9, 10). These infections have become a leading health care concern because of increasing antibiotic resistance mediated by mobile genetic elements (12). The ability of enterococci to colonize extraintestinal sites and cause infection involves both core and variable genetic traits (3, 15) and is not fully understood.Enterococci exhibit diversity in metabolic capabilities (such as the ability of Enterococcus faecalis, but not E. faecium, to respire [11]) and in clinically relevant phenotypes such as toxin production (12) and biofilm formation (13). Enterococci can also be motile or nonmotile, and pigmented or nonpigmented (4), yet little is known about the mechanism and significance of these traits. Insights into basic enterococcal physiology are limited by a paucity of genome data. The genome sequences of the vancomycin-resistant bloodstream isolate E. faecalis V583 (14), the human oral isolate E. faecalis OG1RF (3), and the commercial probiotic strain E. faecalis Symbioflor (6) have been determined, and a draft genome sequence for E. faecium DO has been available in GenBank since 2002. Here we announce the availability of draft genome sequences of 28 additional enterococcal strains, including 16 E. faecalis strains, 8 E. faecium strains, 3 E. casseliflavus strains, and 1 E. gallinarum strain. In addition to expanding the Enterococcus nucleotide sequence in GenBank by approximately an order of magnitude, this is the first report of genome sequencing of the motile E. gallinarum strain and the motile, pigmented E. casseliflavus strains.Most of the enterococcal strains utilized for our genome sequencing project are of clinical origin. The remaining strains are commensal isolates or were obtained from animals or insects. E. faecalis strains selected for this project were previously described in a study of E. faecalis strain diversity (12). To maximize the information yield from genome sequencing, we selected 16 E. faecalis strains that represent the deepest phylogenetic nodes in the E. faecalis multilocus sequence typing (MLST) dendrogram from the 106 strains previously examined (12). These strains include commens...

Current Trends of Emergence and Spread of Vancomycin-Resistant Enterococci

“…Results of a comparative genome-based study revealed a distinct composition of the accessory genome in hospital-associated E. faecium strains (Leavis et al, 2007). Results have been confirmed by recent comparative analyses of completely sequenced E. faecium genomes (van Schaik et al, 2010;Palmer et al, 2010). The current model predicts that spread of ampicillin-resistant, hospital-associated E. faecium strains is a pre-requisite for successful establishment of VRE and further dissemination of vancomycin resistance among the hospital E. faecium population in general Galloway-Pena et al, 2009;Willems and van Schaik W. 2009).…”

SlyA Is a Transcriptional Regulator Involved in the Virulence of Enterococcus faecalis

“…As noted by Wu and collaborators (37), EF_3002 was the most homologous to SlyA-like proteins identified in other species of bacteria and archaea that are involved in virulence and/or stress response. Examination of the currently available sequences of 26 different genomes of E. faecalis shows that the slyA gene is present in each and is part of the core genome of E. faecalis (4,27,28).…”

“…Transcription of EF_3217, encoding a putative helicase, is strongly downregulated in the ⌬slyA mutant. However, it is unlikely that this reduced expression has an impact in the more virulent phenotype of the mutant, because EF_3217 seems to be part of a mobile element and is present in only 5 of the 26 sequenced genomes (4,27,28).…”

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

“…Strain-level analyses of clinical isolates using multilocus sequence typing (MLST) and comparative genomics have been used to differentiate closely related organisms (7,8). However, important contextual information may be lost when interpreting genomic variation between strains isolated from different communities.…”