A genome-wide SNP-based phylogenetic analysis distinguishes different biovars of Brucella suis

Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S.; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

doi:10.1016/j.meegid.2016.04.012

Cited by 27 publications

(22 citation statements)

References 20 publications

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“…Multi-Locus Sequence Analysis (MLSA) based phylogeny using 6 housekeeping genes ( adk , atp A, gyd , gdh , ddl , pur K and pst S) could not distinguish between pathogenic and non-pathogenic strains of E. faecium [95], but this could be achieved by the core genome SNP based phylogeny [96–99]. Thus the phylogenetic reconstruction by using Maximum likelihood method on core genome separated 10 strains in 3 distinct clusters with high bootstrap support (bootstrap > 90) (Fig.…”

Section: Discussionmentioning

confidence: 99%

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

Ghattargi

Gaikwad

Meti³

et al. 2018

BMC Genomics

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BackgroundEnterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains.ResultsE. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal tract was also detected across all the strains.ConclusionsBeyond shared genetic features; this study particularly identified genes that are responsible for imparting probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. Higher genomic stability, absence of known virulence factors and antibiotic resistance genes and close genomic relatedness with marketed probiotics makes E. faecium 17OM39 a potential probiotic candidate. The work presented here demonstrates that comparative genome analyses can be applied to large numbers of genomes, to find potential probiotic candidates.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5043-9) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

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

Ghattargi

Gaikwad

Meti³

et al. 2018

BMC Genomics

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“…Multi-Locus Sequence Analysis (MLSA) based phylogeny could not distinguish between pathogenic and non-pathogenic strains of E. faecium (Homan et al 2002), but this could be achieved on the basis of the core genome SNP based phylogeny (Sankarasubramanian et al 2016; Heydari et al 2013; Chen et al 2013; Vliet and Kusters 2015). Thus, concatenated 1935 core genes were used to construct a phylogenetic tree of the 10 strains along with Enterococcus faecalis symbioflor as an out-group.…”

Section: Resultsmentioning

confidence: 99%

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

Ghattargi

Gaikwad

Meti³

et al. 2018

Preprint

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Enterococcus faecium though commensals in human gut, few strains provide beneficial effect to humans as probiotics, few are responsible for nosocomial infection and few as non-pathogens. Comparative genomics of E. faecium will help to reveal the genomic differences responsible for the said properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. The core genome analysis revealed, 17OM39 was closely related with marketed probiotic strain T110. Strain 17OM39 was found to be devoid of known vancomycin, tetracycline resistance genes and functional virulence genes. Moreover, 17OM39 is „less open‟ due to absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Additional, genes associated with colonization within gastrointestinal tract were detected across all the strains. Beyond shared genetic features; this study particularly identified genes that are responsible to impart probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. The study also provides insights into the acquired and intrinsic drug resistance genes, which will be helpful for better understanding of the physiology of antibiotic resistance in E. faecium strains. In addition, we could identify genes contributing to the intrinsic ability of 17OM39 E. faecium isolate to be a potential probiotic.The study has comprehensively characterized genome sequence of each strain to find the genetic variation and understand effects of these on functionality, phenotypic complexity. Further the evolutionary relationship of species along with adaptation strategies have been including in this study.

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“…Survival and multiplication in macrophages or epithelial cells is affected in T4SS mutants. We must bring up that single nucleotide polymorphism (SNP) performed in the attenuated vaccine strain B. suis S2 shows a mutation occurring in almost all the genes of the virB operon, coding for a type IV secretion system (T4SS), compared with virulent isolates [27].…”

Section: The Pathogenicitymentioning

confidence: 99%

New Scenarios for Brucella suis and Brucella melitensis

Samartino

Arregui

Martino³

2017

Curr Clin Micro Rpt

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Purpose of Review We pretend to highlight the most important advances reached in the last few years in the biology of Brucella suis and Brucella melitensis and focus attention on new tools for the comprehension, prevention and control of these zoonotic agents. Recent Findings Important progress lately done in the field of pathogenesis is presented here. This involves current studies on proteins involved in the survival and antigenic structure of Brucella, as well as the findings of how Brucella has achieved modifications in order to adapt, replicate, survive and modulate the host´s immune system, improve the knowledge of the performance of these bacteria. Summary Consequently, better approaches for vaccinology and diagnostic techniques are developed. Relevant epidemiological issues based on changes in the highly conserved genome of these bacteria will be valuable tools to describe outbreaks and disease status, along with risk factors that would otherwise be difficult to analyze.

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A genome-wide SNP-based phylogenetic analysis distinguishes different biovars of Brucella suis

Cited by 27 publications

References 20 publications

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

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

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

New Scenarios for Brucella suis and Brucella melitensis

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