title: 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.
authors.affiliation: Structural Biology &Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.|Academy of Scientific and Innovative Research (AcSIR), CSIR- Indian Institute of Chemical Biology (CSIR-IICB), 4, Raja S. C. Mullick Road, Kolkata 700032, India.
authors.forename: Utpal
authors.initials: U
authors.lastname: Bakshi
authors.affiliation: Structural Biology &Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
authors.forename: Munmun
authors.initials: M
authors.lastname: Sarkar
authors.affiliation: Structural Biology &Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
authors.forename: Sandip
authors.initials: S
authors.lastname: Paul
authors.affiliation: Structural Biology &Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.|Academy of Scientific and Innovative Research (AcSIR), CSIR- Indian Institute of Chemical Biology (CSIR-IICB), 4, Raja S. C. Mullick Road, Kolkata 700032, India.
authors.forename: Chitra
authors.initials: C
authors.lastname: Dutta
mesh_terms: D001482:Base Composition; D013293:Enterococcus faecalis / Q000145:classification / Q000472:pathogenicity / Q000502:physiology*; D005798:Genes, Bacterial; D014644:Genetic Variation; D059646:Genome Size; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics; D016908:Gram-Positive Bacterial Infections / Q000382:microbiology; D006801:Humans; D016366:Open Reading Frames; D010802:Phylogeny; D010957:Plasmids; D014774:Virulence / Q000235:genetics*; D037521:Virulence Factors / Q000235:genetics
chemical_list: D037521:Virulence Factors