Population Structure of a Hybrid Clonal Group of Methicillin-Resistant Staphylococcus aureus, ST239-MRSA-III
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{"title"=>"Population structure of a hybrid clonal group of methicillin-resistant Staphylococcus aureus, ST239-MRSA-III", "type"=>"journal", "authors"=>[{"first_name"=>"Davida S.", "last_name"=>"Smyth", "scopus_author_id"=>"8276391400"}, {"first_name"=>"Linda K.", "last_name"=>"McDougal", "scopus_author_id"=>"6603925792"}, {"first_name"=>"Frode W.", "last_name"=>"Gran", "scopus_author_id"=>"24740989700"}, {"first_name"=>"Anand", "last_name"=>"Manoharan", "scopus_author_id"=>"7005971557"}, {"first_name"=>"Mark C.", "last_name"=>"Enright", "scopus_author_id"=>"35481958800"}, {"first_name"=>"Jae Hoon", "last_name"=>"Song", "scopus_author_id"=>"7404787802"}, {"first_name"=>"Herminia", "last_name"=>"De Lencastre", "scopus_author_id"=>"7005478837"}, {"first_name"=>"D. Ashley", "last_name"=>"Robinson", "scopus_author_id"=>"8570567000"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"20062529", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0008582", "pui"=>"358372380", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "scopus"=>"2-s2.0-77649084045", "sgr"=>"77649084045"}, "id"=>"7b31e83c-8c55-3fbf-a1a2-84686021e0fd", "abstract"=>"The methicillin-resistant Staphylococcus aureus (MRSA) clonal group known as ST239-MRSA-III is notable for its hybrid origin and for causing sustained hospital epidemics worldwide since the late 1970s. We studied the population structure of this MRSA clonal group using a sample of 111 isolates that were collected over 34 years from 29 countries. Genetic variation was assessed using typing methods and novel ascertainment methods, resulting in approximately 15 kb of sequence from 32 loci for all isolates. A single most parsimonious tree, free of homoplasy, partitioned 28 haplotypes into geographically-associated clades, including prominent European, Asian, and South American clades. The rate of evolution was estimated to be approximately 100x faster than standard estimates for bacteria, and dated the most recent common ancestor of these isolates to the mid-20th century. Associations were discovered between the ST239 phylogeny and the ccrB and dru loci of the methicillin resistance genetic element, SCCmec type III, but not with the accessory components of the element that are targeted by multiplex PCR subtyping tools. In summary, the evolutionary history of ST239 can be characterized by rapid clonal diversification that has left strong evidence of geographic and temporal population structure. SCCmec type III has remained linked to the ST239 chromosome during clonal diversification, but it has undergone homoplasious losses of accessory components. These results provide a population genetics framework for the precise identification of emerging ST239 variants, and invite a re-evaluation of the markers used for subtyping SCCmec.", "link"=>"http://www.mendeley.com/research/population-structure-hybrid-clonal-group-methicillinresistant-staphylococcus-aureus-st239mrsaiii", "reader_count"=>38, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>21, "Medicine and Dentistry"=>6, "Chemistry"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>21}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"Denmark"=>1, "Nigeria"=>1}, "group_count"=>1}

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  • {"files"=>["https://ndownloader.figshare.com/files/431420", "https://ndownloader.figshare.com/files/431505", "https://ndownloader.figshare.com/files/431523", "https://ndownloader.figshare.com/files/431539", "https://ndownloader.figshare.com/files/431575"], "description"=>"<div><p>The methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) clonal group known as ST239-MRSA-III is notable for its hybrid origin and for causing sustained hospital epidemics worldwide since the late 1970s. We studied the population structure of this MRSA clonal group using a sample of 111 isolates that were collected over 34 years from 29 countries. Genetic variation was assessed using typing methods and novel ascertainment methods, resulting in approximately 15 kb of sequence from 32 loci for all isolates. A single most parsimonious tree, free of homoplasy, partitioned 28 haplotypes into geographically-associated clades, including prominent European, Asian, and South American clades. The rate of evolution was estimated to be approximately 100× faster than standard estimates for bacteria, and dated the most recent common ancestor of these isolates to the mid-20th century. Associations were discovered between the ST239 phylogeny and the <em>ccrB</em> and <em>dru</em> loci of the methicillin resistance genetic element, SCC<em>mec</em> type III, but not with the accessory components of the element that are targeted by multiplex PCR subtyping tools. In summary, the evolutionary history of ST239 can be characterized by rapid clonal diversification that has left strong evidence of geographic and temporal population structure. SCC<em>mec</em> type III has remained linked to the ST239 chromosome during clonal diversification, but it has undergone homoplasious losses of accessory components. These results provide a population genetics framework for the precise identification of emerging ST239 variants, and invite a re-evaluation of the markers used for subtyping SCC<em>mec</em>.</p></div>", "links"=>[], "tags"=>["hybrid", "clonal", "methicillin-resistant", "st239-mrsa-iii"], "article_id"=>145142, "categories"=>["Microbiology", "Medicine", "Evolutionary Biology", "Cancer"], "users"=>["Davida S. Smyth", "Linda K. McDougal", "Frode W. Gran", "Anand Manoharan", "Mark C. Enright", "Jae-Hoon Song", "Hermínia de Lencastre", "D. Ashley Robinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0008582.s001", "https://dx.doi.org/10.1371/journal.pone.0008582.s002", "https://dx.doi.org/10.1371/journal.pone.0008582.s003", "https://dx.doi.org/10.1371/journal.pone.0008582.s004", "https://dx.doi.org/10.1371/journal.pone.0008582.s005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Population_Structure_of_a_Hybrid_Clonal_Group_of_Methicillin_Resistant_Staphylococcus_aureus_ST239_MRSA_III/145142", "title"=>"Population Structure of a Hybrid Clonal Group of Methicillin-Resistant <em>Staphylococcus aureus</em>, ST239-MRSA-III", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-01-05 01:25:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/868882"], "description"=>"<p>Tree is the most parsimonious haplotype tree found by heuristic search. Haplotypes are numbered H1–H28. Circles represent the number of isolates of each haplotype. Names of important strains are indicated in parentheses below select haplotypes. Blue labels indicate the discovery panel of isolates. Numbers along branches are bootstrap proportions. Three prominent clades are highlighted.</p>", "links"=>[], "tags"=>["relationships", "st239", "clonal"], "article_id"=>539330, "categories"=>["Microbiology", "Medicine", "Evolutionary Biology", "Virology"], "users"=>["Davida S. Smyth", "Linda K. McDougal", "Frode W. Gran", "Anand Manoharan", "Mark C. Enright", "Jae-Hoon Song", "Hermínia de Lencastre", "D. Ashley Robinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0008582.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_relationships_within_the_ST239_clonal_group_/539330", "title"=>"Evolutionary relationships within the ST239 clonal group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-01-05 02:35:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/868991"], "description"=>"<p>Tree is a neighbor-joining population tree based on the average number of pairwise nucleotide differences between countries. Labels are colored according to continents.</p>", "links"=>[], "tags"=>["st239", "clonal"], "article_id"=>539445, "categories"=>["Microbiology", "Medicine", "Evolutionary Biology", "Virology"], "users"=>["Davida S. Smyth", "Linda K. McDougal", "Frode W. Gran", "Anand Manoharan", "Mark C. Enright", "Jae-Hoon Song", "Hermínia de Lencastre", "D. Ashley Robinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0008582.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographic_structure_within_the_ST239_clonal_group_/539445", "title"=>"Geographic structure within the ST239 clonal group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-01-05 02:37:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/869109"], "description"=>"<p>(A) Mapping of SCC<i>mec</i> multiplex PCR types onto the haplotype tree of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008582#pone-0008582-g001\" target=\"_blank\">Figure 1</a>. (B) Mapping of SCC<i>mec ccrB:dru</i> sequence types onto the haplotype tree of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008582#pone-0008582-g001\" target=\"_blank\">Figure 1</a>. Red highlights homoplasy where two SCC<i>mec</i> subtypes occur together in more than one haplotype.</p>", "links"=>[], "tags"=>["iii"], "article_id"=>539567, "categories"=>["Microbiology", "Medicine", "Evolutionary Biology", "Virology"], "users"=>["Davida S. Smyth", "Linda K. McDougal", "Frode W. Gran", "Anand Manoharan", "Mark C. Enright", "Jae-Hoon Song", "Hermínia de Lencastre", "D. Ashley Robinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0008582.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Homoplasy_among_SCC_mec_type_III_variants_/539567", "title"=>"Homoplasy among SCC<i>mec</i> type III variants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-01-05 02:39:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/869279"], "description"=>"<p>Acronyms: multilocus sequence typing (MLST), <i>Staphylococcus aureus</i> surface protein-encoding gene typing (SAS), previously studied loci (PCR screen), reduced representation shotgun sequencing (RRS).</p><p>77 multiseq contigs were counted as screened.</p><p><i>k<sub>e3</sub></i> is a biased-corrected estimator of the effective number of haplotypes.</p>", "links"=>[], "tags"=>["evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/microbial evolution and genomics", "microbiology/microbial evolution and genomics", "infectious diseases/antimicrobials and drug resistance", "infectious diseases/epidemiology and control of infectious diseases"], "article_id"=>539729, "categories"=>["Microbiology", "Medicine", "Evolutionary Biology", "Virology"], "users"=>["Davida S. Smyth", "Linda K. McDougal", "Frode W. Gran", "Anand Manoharan", "Mark C. Enright", "Jae-Hoon Song", "Hermínia de Lencastre", "D. Ashley Robinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0008582.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_genetic_variation_detected_by_different_datasets_/539729", "title"=>"Summary of genetic variation detected by different datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-01-05 02:42:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/869326"], "description"=>"<p>Correlation is from a regression analysis of tree root-to-haplotype distances versus haplotype dates of isolation. Estimates of the rate of evolution and date of the MRCA are made from the slope and x-intercept, respectively, of the regression line.</p><p>Rate of evolution is in units of 10<sup>−6</sup> nucleotide changes per site per year.</p>", "links"=>[], "tags"=>["evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/microbial evolution and genomics", "microbiology/microbial evolution and genomics", "infectious diseases/antimicrobials and drug resistance", "infectious diseases/epidemiology and control of infectious diseases"], "article_id"=>539773, "categories"=>["Microbiology", "Medicine", "Evolutionary Biology", "Virology"], "users"=>["Davida S. Smyth", "Linda K. McDougal", "Frode W. Gran", "Anand Manoharan", "Mark C. Enright", "Jae-Hoon Song", "Hermínia de Lencastre", "D. Ashley Robinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0008582.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_rate_of_evolution_and_date_of_the_most_recent_common_ancestor_MRCA_/539773", "title"=>"Estimates of rate of evolution and date of the most recent common ancestor (MRCA).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-01-05 02:42:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/869364"], "description"=>"<p>SM tests generally had more taxa per category because all available haplotypes were included, whereas subpopulations that consisted of single haplotypes were not included in SD tests.</p><p>For SM tests, the 29 countries were analyzed as 5 continents weighted by country; one of each haplotype from each country was used. The 42 <i>dru</i> sequences were too diverse to be used with MacClade.</p><p>For SD tests, time's ordered character type was not applicable.</p>", "links"=>[], "tags"=>["clone-corrected"], "article_id"=>539819, "categories"=>["Microbiology", "Medicine", "Evolutionary Biology", "Virology"], "users"=>["Davida S. Smyth", "Linda K. McDougal", "Frode W. Gran", "Anand Manoharan", "Mark C. Enright", "Jae-Hoon Song", "Hermínia de Lencastre", "D. Ashley Robinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0008582.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analyses_of_population_structure_using_clone_corrected_datasets_/539819", "title"=>"Analyses of population structure using clone-corrected datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-01-05 02:43:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/869392"], "description"=>"<p><i>k<sub>e3</sub></i> is a biased-corrected estimator of the effective number of SCC<i>mec</i> variants.</p>", "links"=>[], "tags"=>["iii", "typing"], "article_id"=>539845, "categories"=>["Microbiology", "Medicine", "Evolutionary Biology", "Virology"], "users"=>["Davida S. Smyth", "Linda K. McDougal", "Frode W. Gran", "Anand Manoharan", "Mark C. Enright", "Jae-Hoon Song", "Hermínia de Lencastre", "D. Ashley Robinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0008582.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SCC_mec_type_III_variation_as_detected_by_different_typing_methods_/539845", "title"=>"SCC<i>mec</i> type III variation as detected by different typing methods.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-01-05 02:44:05"}

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  • {"unique-ip"=>"20", "full-text"=>"13", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2014", "month"=>"9"}
  • {"unique-ip"=>"14", "full-text"=>"10", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
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  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"4", "year"=>"2015", "month"=>"11"}
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  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
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  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
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  • {"unique-ip"=>"7", "full-text"=>"6", "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"=>"4", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"8", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"2", "year"=>"2017", "month"=>"1"}
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  • {"unique-ip"=>"4", "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"=>"7"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
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  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "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"=>"4", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
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  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
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  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"6", "full-text"=>"7", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"4", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
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  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
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Relative Metric

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