Evolutionary Analyses of Staphylococcus aureus Identify Genetic Relationships between Nasal Carriage and Clinical Isolates
Publication Date
January 21, 2011
Journal
PLOS ONE
Authors
Ryan P. Lamers, Jason W. Stinnett, Gowrishankar Muthukrishnan, Christopher L. Parkinson, et al
Volume
6
Issue
1
Pages
e16426
DOI
http://doi.org/10.1371/journal.pone.0016426
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0016426
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21283661
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025037
Europe PMC
http://europepmc.org/abstract/MED/21283661
Web of Science
000286522300047
Scopus
79251639362
Mendeley
http://www.mendeley.com/research/evolutionary-analyses-staphylococcus-aureus-identify-genetic-relationships-between-nasal-carriage-cl
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/805019"], "description"=>"<p>Double-ended arrows indicate region of analysis for this study. For <i>clf</i> genes: S, signal sequence; A, fibrinogen/fibronectin-binding domain; R, serine-aspartic acid repeat region; W, wall spanning domain; M, membrane spanning domain. For <i>fnb</i> genes: S, signal sequence; A, fibrinogen-binding domain; B, region containing 2 repeats of unknown function (only present in <i>fnbA</i>); C, region containing Du repeats with fibronectin-binding activity; D, region containing 4–5 repeats with fibronectin-binding activity; Wr, proline-rich repeat region of the wall spanning domain; Wc, constant region of the wall spanning domain; M, membrane spanning domain.</p>", "links"=>[], "tags"=>["Infectious diseases", "microbiology", "respiratory medicine", "otolaryngology"], "article_id"=>475387, "categories"=>["Microbiology", "Medicine", "Infectious Diseases"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016426.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_structure_of_clf_and_fnb_/475387", "title"=>"Genetic structure of <i>clf</i> and <i>fnb</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-21 01:29:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/805199"], "description"=>"<p>(A) <i>clfA</i>, N = 52 nasal carriage and 28 clinical isolates; (B) <i>clfB</i>, N = 61 nasal carriage and 28 clinical isolates; (C) <i>fnbA</i>, N = 63 nasal carriage and 27 clinical isolates; and (D) <i>fnbB</i>, N = 56 nasal carriage and 11 clinical isolates.</p>", "links"=>[], "tags"=>["strains", "reveals", "lineage", "associations", "nasal", "carriage"], "article_id"=>475564, "categories"=>["Microbiology", "Medicine", "Infectious Diseases"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016426.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classification_of_S_aureus_strains_reveals_lineage_associations_between_nasal_carriage_and_clinical_isolates_/475564", "title"=>"Classification of <i>S. aureus</i> strains reveals lineage associations between nasal carriage and clinical isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-21 01:32:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/401939", "https://ndownloader.figshare.com/files/401998", "https://ndownloader.figshare.com/files/402071", "https://ndownloader.figshare.com/files/402121", "https://ndownloader.figshare.com/files/402237", "https://ndownloader.figshare.com/files/402287", "https://ndownloader.figshare.com/files/402340", "https://ndownloader.figshare.com/files/402407", "https://ndownloader.figshare.com/files/402466", "https://ndownloader.figshare.com/files/402515", "https://ndownloader.figshare.com/files/402558"], "description"=>"<div><p>Nasal carriage of <em>Staphylococcus aureus</em> has long been hypothesized to be a major vector for the transmission of virulent strains throughout the community. To address this hypothesis, we have analyzed the relatedness between a cohort of nasal carriage strains and clinical isolates to understand better the genetic conformity therein. To assess the relatedness between nasal carriage and clinical isolates of <em>S. aureus</em>, a genetic association study was conducted using multilocus sequence typing (MLST) and typing of the hypervariable regions of clumping factor and fibronectin binding protein genes. At all loci analyzed, genetic associations between both nasal carriage and clinical isolates were observed. Computational analyses of MLST data indicate that nasal carriage and clinical isolates belong to the same genetic clusters (clades), despite differences in sequence type assignments. Genetic analyses of the hypervariable regions from the clumping factor and fibronectin binding protein genes revealed that not only do clinically relevant strains belong to identical genetic lineages as the nasal carriage isolates within our cohort, but they also exhibit 100% sequence similarity within these regions. The findings of this report indicate that strains of <em>S. aureus</em> being carried asymptomatically throughout the community via nasal colonization are genetically related to those responsible for high levels of morbidity and mortality.</p> </div>", "links"=>[], "tags"=>["evolutionary", "analyses", "relationships", "nasal", "carriage", "isolates"], "article_id"=>139413, "categories"=>["Medicine", "Cancer", "Microbiology"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0016426.s001", "https://dx.doi.org/10.1371/journal.pone.0016426.s002", "https://dx.doi.org/10.1371/journal.pone.0016426.s003", "https://dx.doi.org/10.1371/journal.pone.0016426.s004", "https://dx.doi.org/10.1371/journal.pone.0016426.s005", "https://dx.doi.org/10.1371/journal.pone.0016426.s006", "https://dx.doi.org/10.1371/journal.pone.0016426.s007", "https://dx.doi.org/10.1371/journal.pone.0016426.s008", "https://dx.doi.org/10.1371/journal.pone.0016426.s009", "https://dx.doi.org/10.1371/journal.pone.0016426.s010", "https://dx.doi.org/10.1371/journal.pone.0016426.s011"], "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Evolutionary_Analyses_of_Staphylococcus_aureus_Identify_Genetic_Relationships_between_Nasal_Carriage_and_Clinical_Isolates/139413", "title"=>"Evolutionary Analyses of <em>Staphylococcus aureus</em> Identify Genetic Relationships between Nasal Carriage and Clinical Isolates", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-01-21 02:36:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/805539"], "description"=>"<p>Diversity indices for virulence genes analyzed in this study.</p>", "links"=>[], "tags"=>["indices", "virulence", "genes"], "article_id"=>475907, "categories"=>["Microbiology", "Medicine", "Infectious Diseases"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016426.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_indices_for_virulence_genes_analyzed_in_this_study_/475907", "title"=>"Diversity indices for virulence genes analyzed in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-21 01:38:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/805445"], "description"=>"<p>Note that identical sequences are evident between both nasal carriage and clinical isolates. D1–D4, repeat region containing fibronectin-binding activity; Wr1–Wr7, proline-rich repeat region of the wall spanning domain; Wc, constant region of the wall spanning domain. Isolate names written in black are nasal carriage strains and those written in red are clinical strains. Regions of amino acid variability are shaded grey and underlined.</p>", "links"=>[], "tags"=>["fnba", "amino", "sequences", "nasal", "carriage"], "article_id"=>475810, "categories"=>["Microbiology", "Medicine", "Infectious Diseases"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016426.g007", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_FnbA_amino_acid_sequences_between_four_representative_nasal_carriage_and_four_representative_clinical_S_aureus_isolates_/475810", "title"=>"Comparison of FnbA amino acid sequences between four representative nasal carriage and four representative clinical <i>S. aureus</i> isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-21 01:36:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/804874"], "description"=>"<p>STs written in black are nasal carriage strains, those written in red are clinical strains and STs written in green indicate both nasal carriage and clinical isolates are contained within. (A) eBURST application of MLST data from all isolates analyzed in this study. Numbers represent ST. STs that are linked by a line belong to the same cluster. Circle sizes are proportional to the number of strains within the ST. (B) Minimal spanning network of MLST data from the same isolates analyzed in (A). Circles represent STs with the numbers within. Branches represent a single nucleotide change between neighboring STs. Black squares indicate multiple nucleotide changes between adjoining STs with the number of differences indicated by the adjacent numbers. Like-colored circles represent STs belonging to the same cluster, as in (A). Non-colored circles are singletons by eBURST analysis.</p>", "links"=>[], "tags"=>["carriage", "isolates"], "article_id"=>475246, "categories"=>["Microbiology", "Medicine", "Infectious Diseases"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016426.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nasal_carriage_and_clinical_isolates_of_S_aureus_belong_to_the_same_genetic_clusters_/475246", "title"=>"Nasal carriage and clinical isolates of <i>S. aureus</i> belong to the same genetic clusters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-21 01:27:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/805113"], "description"=>"<p>Shown are Box and Whisker plots comparing repeat domain lengths between nasal carriage strains of <i>S. aureus</i> and clinical strains. (A) Repeat domain lengths compared at <i>clf</i> loci; and (B) repeat domain lengths compared at <i>fnb</i> loci.</p>", "links"=>[], "tags"=>["lengths", "genes", "indistinguishable", "nasal", "carriage"], "article_id"=>475479, "categories"=>["Microbiology", "Medicine", "Infectious Diseases"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016426.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Repeat_domain_lengths_of_clf_and_fnb_genes_are_indistinguishable_between_nasal_carriage_and_clinical_isolates_/475479", "title"=>"Repeat domain lengths of <i>clf</i> and <i>fnb</i> genes are indistinguishable between nasal carriage and clinical isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-21 01:31:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/805310"], "description"=>"<p>Shown are <i>clf</i> repeat regions represented as color-coded bars. Like-colored boxes indicate 100% sequence similarity between isolates. (A) <i>clfA</i> and (B) <i>clfB</i> repeat region sequences from a representative sampling of all isolates analyzed within this study. Isolate names written in black are nasal carriage strains and those written in red are clinical strains.</p>", "links"=>[], "tags"=>["carriage", "isolates"], "article_id"=>475681, "categories"=>["Microbiology", "Medicine", "Infectious Diseases"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016426.g006", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nasal_carriage_and_clinical_isolates_of_S_aureus_share_near_identical_clf_repeat_region_sequences_/475681", "title"=>"Nasal carriage and clinical isolates of <i>S. aureus</i> share (near-)identical <i>clf</i> repeat region sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-21 01:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/804706"], "description"=>"<p>Bayesian phylogram indicating the evolutionary relationships of <i>S. aureus</i> strains analyzed in this study. Represented are 66 nasal carriage strains (strains colored in black) and 27 clinical strains (strains colored in red). Note that several clinical isolates cluster on the same genetic clade as major clinical strains. Numbers represent posterior probabilities and grey-filled circles represent nodes receiving 100% posterior probability support. Colored boxes are consistent with strain groupings in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016426#pone-0016426-g002\" target=\"_blank\">Figure 2</a> (below).</p>", "links"=>[], "tags"=>["reveals", "phylogenetic", "relationships", "nasal", "carriage"], "article_id"=>475071, "categories"=>["Microbiology", "Medicine", "Infectious Diseases"], "users"=>["Ryan P. Lamers", "Jason W. Stinnett", "Gowrishankar Muthukrishnan", "Christopher L. Parkinson", "Alexander M. Cole"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016426.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MLST_analysis_reveals_phylogenetic_relationships_between_S_aureus_nasal_carriage_and_clinical_strains_/475071", "title"=>"MLST analysis reveals phylogenetic relationships between <i>S. aureus</i> nasal carriage and clinical strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-21 01:24:31"}

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Relative Metric

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