The Transcriptome of the Nosocomial Pathogen Enterococcus faecalis V583 Reveals Adaptive Responses to Growth in Blood
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{"title"=>"The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood", "type"=>"journal", "authors"=>[{"first_name"=>"Heidi C.", "last_name"=>"Vebø", "scopus_author_id"=>"8628922700"}, {"first_name"=>"Lars", "last_name"=>"Snipen", "scopus_author_id"=>"8684985700"}, {"first_name"=>"Ingolf F.", "last_name"=>"Nes", "scopus_author_id"=>"7005100689"}, {"first_name"=>"Dag A.", "last_name"=>"Brede", "scopus_author_id"=>"35077581600"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-70449427943", "sgr"=>"70449427943", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0007660", "pmid"=>"19888459", "isbn"=>"1932-6203", "pui"=>"355609621"}, "id"=>"b36a11e1-2a21-38b4-83cc-bfce9a950231", "abstract"=>"BACKGROUND: Enterococcus faecalis plays a dual role in human ecology, predominantly existing as a commensal in the alimentary canal, but also as an opportunistic pathogen that frequently causes nosocomial infections like bacteremia. A number of virulence factors that contribute to the pathogenic potential of E. faecalis have been established. However, the process in which E. faecalis gains access to the bloodstream and establishes a persistent infection is not well understood. METHODOLOGY/PRINCIPAL FINDINGS: To enhance our understanding of how this commensal bacterium adapts during a bloodstream infection and to examine the interplay between genes we designed an in vitro experiment using genome-wide microarrays to investigate what effects the presence of and growth in blood have on the transcriptome of E. faecalis strain V583. We showed that growth in both 2xYT supplemented with 10% blood and in 100% blood had a great impact on the transcription of many genes in the V583 genome. We identified several immediate changes signifying cellular processes that might contribute to adaptation and growth in blood. These include modulation of membrane fatty acid composition, oxidative and lytic stress protection, acquisition of new available substrates, transport functions including heme/iron transporters and genes associated with virulence in E. faecalis. CONCLUSIONS/SIGNIFICANCE: The results presented here reveal that cultivation of E. faecalis in blood in vitro has a profound impact on its transcriptome, which includes a number of virulence traits. Observed regulation of genes and pathways revealed new insight into physiological features and metabolic capacities which enable E. faecalis to adapt and grow in blood. A number of the regulated genes might potentially be useful candidates for development of new therapeutic approaches for treatment of E. faecalis infections.", "link"=>"http://www.mendeley.com/research/transcriptome-nosocomial-pathogen-enterococcus-faecalis-v583-reveals-adaptive-responses-growth-blood", "reader_count"=>60, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>7, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>7, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>37, "Medicine and Dentistry"=>5, "Design"=>1, "Chemistry"=>2, "Immunology and Microbiology"=>3, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Chemistry"=>{"Chemistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>37}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Peru"=>1}, "group_count"=>1}

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  • {"files"=>["https://ndownloader.figshare.com/files/876813"], "description"=>"<p>List of genes and primers (5′→ 3′) used for real-time quantitative RT-PCR.</p>", "links"=>[], "tags"=>["genes", "primers", "Real-time", "quantitative"], "article_id"=>547269, "categories"=>["Microbiology", "Genetics", "Cell Biology", "Biochemistry", "Infectious Diseases", "Medicine", "Molecular Biology", "Biotechnology"], "users"=>["Heidi C. Vebø", "Lars Snipen", "Ingolf F. Nes", "Dag A. Brede"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007660.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_genes_and_primers_5_8242_8594_3_8242_used_for_real_time_quantitative_RT_PCR_/547269", "title"=>"List of genes and primers (5′→ 3′) used for real-time quantitative RT-PCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-04 02:01:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/876492"], "description"=>"<p>Growth of <i>E. faecalis</i> V583 was determined from cultures pre-cultivated in 2xYT, and transferred to a fresh medium (either 2xYT, YTB or blood). The growth curves are represented by colony forming units per millilitre (CFU/ml) on the Y-axis, and minutes as indicated on the X-axis. The growth curves correspond to the mean ± STD of three individual experiments. Arrows indicate the time points when samples were harvested prior to RNA extraction. Samples from 2xYT were harvested either only after 30 minutes (when compared to blood), or after 5, 15, 30 and 60 minutes (when compared to YTB).</p>", "links"=>[], "tags"=>["v583", "ytb"], "article_id"=>546950, "categories"=>["Microbiology", "Genetics", "Cell Biology", "Biochemistry", "Infectious Diseases", "Medicine", "Molecular Biology", "Biotechnology"], "users"=>["Heidi C. Vebø", "Lars Snipen", "Ingolf F. Nes", "Dag A. Brede"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007660.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characterization_of_E_faecalis_V583_growth_in_2xYT_YTB_and_blood_/546950", "title"=>"Characterization of <i>E. faecalis</i> V583 growth in 2xYT, YTB and blood.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-04 01:55:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/434795"], "description"=>"<div><h3>Background</h3><p><em>Enterococcus faecalis</em> plays a dual role in human ecology, predominantly existing as a commensal in the alimentary canal, but also as an opportunistic pathogen that frequently causes nosocomial infections like bacteremia. A number of virulence factors that contribute to the pathogenic potential of <em>E. faecalis</em> have been established. However, the process in which <em>E. faecalis</em> gains access to the bloodstream and establishes a persistent infection is not well understood.</p><h3>Methodology/Principal Findings</h3><p>To enhance our understanding of how this commensal bacterium adapts during a bloodstream infection and to examine the interplay between genes we designed an <em>in vitro</em> experiment using genome-wide microarrays to investigate what effects the presence of and growth in blood have on the transcriptome of <em>E. faecalis</em> strain V583. We showed that growth in both 2xYT supplemented with 10% blood and in 100% blood had a great impact on the transcription of many genes in the V583 genome. We identified several immediate changes signifying cellular processes that might contribute to adaptation and growth in blood. These include modulation of membrane fatty acid composition, oxidative and lytic stress protection, acquisition of new available substrates, transport functions including heme/iron transporters and genes associated with virulence in <em>E. faecalis</em>.</p><h3>Conclusions/Significance</h3><p>The results presented here reveal that cultivation of <em>E. faecalis</em> in blood <em>in vitro</em> has a profound impact on its transcriptome, which includes a number of virulence traits. Observed regulation of genes and pathways revealed new insight into physiological features and metabolic capacities which enable <em>E. faecalis</em> to adapt and grow in blood. A number of the regulated genes might potentially be useful candidates for development of new therapeutic approaches for treatment of <em>E. faecalis</em> infections.</p></div>", "links"=>[], "tags"=>["transcriptome", "nosocomial", "pathogen", "v583", "reveals", "adaptive", "responses"], "article_id"=>145767, "categories"=>["Microbiology", "Genetics", "Cell Biology", "Biochemistry", "Cancer", "Medicine", "Molecular Biology", "Biotechnology"], "users"=>["Heidi C. Vebø", "Lars Snipen", "Ingolf F. Nes", "Dag A. Brede"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007660", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Transcriptome_of_the_Nosocomial_Pathogen_Enterococcus_faecalis_V583_Reveals_Adaptive_Responses_to_Growth_in_Blood/145767", "title"=>"The Transcriptome of the Nosocomial Pathogen <em>Enterococcus faecalis</em> V583 Reveals Adaptive Responses to Growth in Blood", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-04 01:36:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/876693"], "description"=>"<p>The asterisks indicate values from the microarray experiments that were found to be outside the rejection level. The corresponding orf-numbers for the genes tested are: <i>lrgB</i>; EF3193, <i>fabI</i>; EF0285, <i>fabK</i>; EF2883, <i>fabT</i>; EF2886, <i>bopA</i>; EF0957, <i>efaA</i>; EF2076, <i>dltA</i>; EF2749, cpsC; EF2493 ace; EF1099, <i>gelE</i>; EF1818, <i>fsrB</i>; EF1821.</p>", "links"=>[], "tags"=>["30", "minutes", "ytb", "compared", "2xyt", "microarray", "Real-time", "quantitative"], "article_id"=>547143, "categories"=>["Microbiology", "Genetics", "Cell Biology", "Biochemistry", "Infectious Diseases", "Medicine", "Molecular Biology", "Biotechnology"], "users"=>["Heidi C. Vebø", "Lars Snipen", "Ingolf F. Nes", "Dag A. Brede"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007660.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_regulation_log_2_after_30_minutes_growth_in_either_blood_or_YTB_compared_to_2xYT_analyzed_by_microarray_or_real_time_quantitative_RT_PCR_/547143", "title"=>"Gene regulation (log<sub>2</sub>) after 30 minutes growth in either blood or YTB compared to 2xYT analyzed by microarray or real-time quantitative RT-PCR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-04 01:59:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/876566"], "description"=>"<p>Genes found to be significantly regulated are indicated by either red (up-regulated), or green (down-regulated). Genes regulated after growth for 30 minutes in blood, compared to in 2xYT are listed in column 1. Genes regulated during growth in YTB compared to 2xYT are listed in columns 2–4, time-points in minutes indicated on the top of each column. The genes are sorted alphabetically by functional categories (column 5).</p>", "links"=>[], "tags"=>["visualizing", "regulated", "genes", "v583", "grown", "ytb", "compared"], "article_id"=>547022, "categories"=>["Microbiology", "Genetics", "Cell Biology", "Biochemistry", "Infectious Diseases", "Medicine", "Molecular Biology", "Biotechnology"], "users"=>["Heidi C. Vebø", "Lars Snipen", "Ingolf F. Nes", "Dag A. Brede"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007660.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_map_visualizing_regulated_genes_in_V583_grown_in_blood_and_YTB_compared_to_growth_in_2xYT_/547022", "title"=>"Heat map visualizing regulated genes in V583 grown in blood and YTB compared to growth in 2xYT.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-04 01:57:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/876857"], "description"=>"<p>*The corresponding p-value was above the chosen level of statistical significance. However the up-regulation of this gene was confirmed by real-time QPCR (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007660#pone-0007660-g003\" target=\"_blank\">Fig. 3</a>).</p>", "links"=>[], "tags"=>["proven", "virulence", "v583", "regulated"], "article_id"=>547311, "categories"=>["Microbiology", "Genetics", "Cell Biology", "Biochemistry", "Infectious Diseases", "Medicine", "Molecular Biology", "Biotechnology"], "users"=>["Heidi C. Vebø", "Lars Snipen", "Ingolf F. Nes", "Dag A. Brede"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007660.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_proven_or_predicted_to_be_important_for_virulence_in_V583_found_to_be_regulated_during_growth_in_blood_/547311", "title"=>"Genes proven or predicted to be important for virulence in V583 found to be regulated during growth in blood.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-04 02:01:51"}

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  • {"unique-ip"=>"5", "full-text"=>"7", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
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  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
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  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"9", "full-text"=>"11", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
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  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
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  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
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  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
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  • {"unique-ip"=>"13", "full-text"=>"17", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"12", "full-text"=>"18", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"12", "full-text"=>"13", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
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  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
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  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"16", "full-text"=>"17", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"2", "cited-by"=>"1", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"10", "full-text"=>"7", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"11", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"18", "full-text"=>"20", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"14", "full-text"=>"21", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
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Relative Metric

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