Abstract
BackgroundEnterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type.ResultsWe compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated. D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro).ConclusionMolecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1367-x) contains supplementary material, which is available to authorized users.
Highlights
Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium
Presence and expression of putative virulenceassociated genes encoded within the E. faecalis pathogenicity island (PAI) and/or on the chromosome were investigated by PCR and partly confirmed by phenotypic in vitro assays (Table 4)
This indicates that genomic variability within clonal types or lineages may be limited, which is in line with previous reports [49] and which does not contradict the general observation of a high level of recombination at the level of Enterococcus faecalis species
Summary
Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Recent studies on livestock animals have improved our understanding of the role enterococci play as important intestinal colonisers by supporting intestinal, microbial homoeostasis, stimulating immune modulation and preventing infections with pathogenic bacteria and viruses [1,2,3]. Commercial probiotic mixtures of Enterococcus faecalis are sold with a supposed supportive role in anti-inflammation and prevention of allergic reactions. E. faecalis has been attributed to various kinds of infections in humans in hospitals and in the community such as urinary tract infections, bacteraemia and/or endocarditis [6,7,8,9].a In animals it is a common cause of mastitis in cattle [10], and of urinary tract infections in dogs and cats
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