Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island

Abstract

BackgroundThe Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients.ResultsWe present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI), which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner.ConclusionsGenes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.

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).…”

“…These strains can be assigned to distinct clonal groups or complexes based on various molecular typing schemes and subsequent phylogenetic analyses (Willems and van Schaik W. 2009;Willems et al, 2011). Hospitalacquired E. faecium are mostly ampicillin-resistant, partly high-level ciprofloxacin-resistant and possess additional genomic content (accessory genome), which includes putative virulence traits such as a gene for an enterococcal surface protein, esp, genes encoding different cell wall-anchored surface proteins, a putative hyaluronidase gene, hyl Efm and a gene encoding a collagen-binding protein, acm Leavis et al, 2007;Hendrickx et al, 2007;Hendrickx et al, 2008;Heikens et al, 2008;Sillanpaa et al, 2008;Nallapareddy et al, 2008;Hendrickx et al, 2009;van Schaik et al, 2010;Laverde Gomez et al, 2010;van Schaik and Willems 2010).…”

Antibacterial and antioxidant activities of bilberry (Vaccinium myrtillus L.) in vitro

“…Enterococci are Gram-positive commensals of the gastrointestinal tract of humans. E. faecalis is an important cause of infections in hospitalized, immunocompromized patients (Schaik et al, 2010). Proteus species have an important place in environmental pollution bioremediation.…”

The interactions between esp, fsr, gelE genes and biofilm formation and pfge analysis of clinical Enterococcus faecium strains

“…faecium and Enterococcus. faecalis (van Schaik et al, 2010). Contrary to most of lactic acid bacteria, enterococci are not considered "generally recognized as safe (GRAS)" because of they are considered to be pathogens with low virulence (Hallgren et al, 2003;Ogier and Serror, 2008).…”