Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach – Identification of pathogen–specific and habitat-specific genes

Abstract

Enterococcus faecalis, a leading nosocomial pathogen and yet a prominent member of gut microbiome, lacks clear demarcation between pathogenic and non-pathogenic strains at genome level. Here we present the comparative genome analysis of 36 E. faecalis strains with different pathogenic features and from different body-habitats. This study begins by addressing the genome dynamics, which shows that the pan-genome of E. faecalis is still open, though the core genome is nearly saturated. We identified eight uncharacterized strains as potential pathogens on the basis of their co-segregation with reported pathogens in gene presence-absence matrix and Pathogenicity Island (PAI) distribution. A ~7.4 kb genomic-cassette, which is itself a part of PAI, is found to exist in all reported and potential pathogens, but not in commensals and other uncharacterized strains. This region encodes four genes and among them, products of two hypothetical genes are predicted to be intrinsically disordered that may serve as novel targets for therapeutic measures. Exclusive existence of 215, 129, 4 and 1 genes in the blood, gastrointestinal tract, urogenital tract, oral cavity and lymph node derived E. faecalis genomes respectively suggests possible employment of distinct habitat-specific genetic strategies in the adaptation of E. faecalis in human host.

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

“…These results are in accordance with the previous study for E. faecium genome [36]. The small size of core genome and huge number of accessory genes support the observation of the genomic fluidity in E. faecium [37]. …”

Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF

“…Genomic analysis of commensal and infection-associated E. faecalis strains reveals a highly conserved (in terms of both synteny and protein sequences) core of approximately 2,500 genes, with a preponderance of additional mobile elements (plasmids, transposons [Tns], and genomic islands) encoding antibiotic resistance and suspected virulence determinants involved in hospital outbreaks ( 4 , 5 ). Recently, an elegant phylogenetic analysis of genome sequences from 24 diverse enterococcal species and five closely related nonenterococcal species suggested that enterococci have coevolved as GI tract commensals with terrestrial animals since the time of their divergence from fish ( 6 ).…”

Comparative Genome Analysis Reveals Important Genetic Factors Associated with Probiotic Property inEnterococcus faeciumstrains

“…Thus, the analysis conducted here has shown that pan-genome of E. faecium constructed on the basis of 10 genomes is still open, while the core genome seems to have reached almost a closed state. The small size of the core genome and a huge number of accessory genes support the observation of the genomic fluidity of E. faecium (Bakshi et al 2016).…”