Phylogenetic Incongruence in E. coli O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination
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{"title"=>"Phylogenetic incongruence in E. coli O104: Understanding the evolutionary relationships of emerging pathogens in the face of homologous recombination", "type"=>"journal", "authors"=>[{"first_name"=>"Weilong", "last_name"=>"Hao", "scopus_author_id"=>"7101686536"}, {"first_name"=>"Vanessa G.", "last_name"=>"Allen", "scopus_author_id"=>"23392251500"}, {"first_name"=>"Frances B.", "last_name"=>"Jamieson", "scopus_author_id"=>"7004189295"}, {"first_name"=>"Donald E.", "last_name"=>"Low", "scopus_author_id"=>"56870843600"}, {"first_name"=>"David C.", "last_name"=>"Alexander", "scopus_author_id"=>"7402830427"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84859509675", "sgr"=>"84859509675", "pui"=>"364590409", "isbn"=>"1932-6203", "pmid"=>"22493677", "doi"=>"10.1371/journal.pone.0033971"}, "id"=>"e4ddb01e-540e-3b99-b982-769530f31d0c", "abstract"=>"Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678), but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen.", "link"=>"http://www.mendeley.com/research/phylogenetic-incongruence-e-coli-o104-understanding-evolutionary-relationships-emerging-pathogens-fa", "reader_count"=>36, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>2, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>3, "Australia"=>1, "France"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/337581", "https://ndownloader.figshare.com/files/337621", "https://ndownloader.figshare.com/files/337659", "https://ndownloader.figshare.com/files/337702", "https://ndownloader.figshare.com/files/337770", "https://ndownloader.figshare.com/files/337864"], "description"=>"<div><p><em>Escherichia coli</em> O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of <em>E. coli</em> O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678), but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related <em>E. coli</em> strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen.</p> </div>", "links"=>[], "tags"=>["phylogenetic", "incongruence", "evolutionary", "relationships", "pathogens", "homologous", "recombination"], "article_id"=>126727, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.s001", "https://dx.doi.org/10.1371/journal.pone.0033971.s002", "https://dx.doi.org/10.1371/journal.pone.0033971.s003", "https://dx.doi.org/10.1371/journal.pone.0033971.s004", "https://dx.doi.org/10.1371/journal.pone.0033971.s005", "https://dx.doi.org/10.1371/journal.pone.0033971.s006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenetic_Incongruence_in_E_coli_O104_Understanding_the_Evolutionary_Relationships_of_Emerging_Pathogens_in_the_Face_of_Homologous_Recombination/126727", "title"=>"Phylogenetic Incongruence in <em>E. coli</em> O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-04-06 01:52:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/656832"], "description"=>"<p><i>E. fergusonii</i> was chosen to root the tree. Three internal branches that are not well supported (with a bootstrap value <90) are labeled as asterisks. Phylogenetic group membership of the strains is indicated with bars at the right of the figure. The <i>E. coli</i> O104 strains are shaded.</p>", "links"=>[], "tags"=>["phylogenetic", "58", "strains", "reconstructed", "sequences", "2085", "universally", "single-copy", "genes", "characters"], "article_id"=>327304, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenetic_tree_of_the_58_Escherichia_and_Shigella_strains_57_E_coli_Shigella_E_fergusonii_as_reconstructed_from_the_sequences_of_2085_universally_present_single_copy_genes_1962650_characters_in_total_/327304", "title"=>"Maximum likelihood phylogenetic tree of the 58 <i>Escherichia</i> and <i>Shigella</i> strains (57 <i>E. coli/Shigella</i> + <i>E. fergusonii</i>) as reconstructed from the sequences of 2085 universally present single-copy genes (1962650 characters in total).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:01:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/656925"], "description"=>"<p>A), all 2085 universally present genes were analyzed. B), universally present recombinant genes were excluded. Proportions of ancestry were inferred using STRUCTURE <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033971#pone.0033971-Falush1\" target=\"_blank\">[35]</a> by assuming four groups (K = 4), and displayed with DISTRUCT <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033971#pone.0033971-Rosenberg1\" target=\"_blank\">[67]</a>. Each column represents one genome, and the genome order is as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033971#pone-0033971-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["clusters"], "article_id"=>327413, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_clusters_of_the_Escherichia_and_Shigella_strains_/327413", "title"=>"Population clusters of the <i>Escherichia</i> and <i>Shigella</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:03:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/657012"], "description"=>"<p>A), maximum likelihood tree of the concatenated sequences (3613248 characters). All branches are 100% bootstrap supported. The branch length separating IAI1 from the <i>E. coli</i> O104:H4 strains is not to scale and the length is shown. B), feature frequency profiles (FFPs) tree. ON2010 is shown to be distinct from the remaining <i>E. coli</i> O104:H4 strains and IAI1. The branch length separating ON2010 from other strains is not to scale and the length is shown. C), neighbor-joining tree based on the number of alleles that differ between any two strains. D), neighbor-joining tree based on the number of alleles that have none-zero DNA distance between any two strains. Unlike in C, small indels, including possible homopolymer sequencing errors, were not considered in D.</p>", "links"=>[], "tags"=>["phylogenies", "constructed", "3794", "genes"], "article_id"=>327495, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_E_coli_O104_H4_phylogenies_constructed_based_on_the_3794_shared_genes_using_different_methodologies_/327495", "title"=>"<i>E. coli</i> O104:H4 phylogenies constructed based on the 3794 shared genes using different methodologies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:04:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/657072"], "description"=>"<p>De novo whole genome optical maps from the ON2010 and ON2011 strains were generated using the Argus™ optical mapping system with the <i>Ncol</i> restriction enzyme. An in silico genomic map of the 55989 strain was generated in MapSolver™ by applying the <i>Ncol</i> restriction pattern. A close relationship between LB226692 and 01-09591 was reported by Mellmann <i>et al.</i> 2011 using the same restriction enzyme, and the 01-09591 branch is added as dashed.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Computational biology", "Evolutionary biology"], "article_id"=>327555, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optical_map_similarity_cluster_of_the_E_coli_O104_H4_strains_/327555", "title"=>"Optical map similarity cluster of the <i>E. coli</i> O104:H4 strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:05:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/657128"], "description"=>"<p>(A) 55989 vs. ON2010; (B) 55989 vs. IAI1. Homologous matches are taken to have an expected value <10<sup>−20</sup> for all the 3792 genes shared by IAI1, 55989, 01-09591, ON2010 and ON2011 in a BLASTN search. The x-axis shows the order of genes on the 55989 chromosome. The y-axis shows the nucleotide coordinates of the subject genome.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Computational biology", "Evolutionary biology"], "article_id"=>327610, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_synteny_/327610", "title"=>"Genome synteny.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:06:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/657183"], "description"=>"<p>The data are plotted as of the gene order on the 55989 chromosome.</p>", "links"=>[], "tags"=>["on2010", "55989"], "article_id"=>327664, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DNA_distance_between_ON2010_vs_55989_and_between_ON2010_vs_01_09591_/327664", "title"=>"DNA distance between ON2010 vs. 55989 and between ON2010 vs. 01-09591.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:07:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/657238"], "description"=>"<p>The functional categories are information storage and processing, including COG categories J, K, L, and B; cellular processes and signaling, including V, T, M, N, U, and O; metabolism, including C, G, E, F, H, I, P, and Q; poorly characterized including R and S; and ‘-’ refers to not in COG.</p>", "links"=>[], "tags"=>["categories", "125", "genes", "on2010-specific"], "article_id"=>327717, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_COG_functional_categories_of_the_125_genes_involved_in_ON2010_specific_recombination_/327717", "title"=>"COG functional categories of the 125 genes involved in ON2010-specific recombination.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:08:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/657331"], "description"=>"<p>A), maximum likelihood tree of the concatenated sequences of 3669 genes (3487410 characters). All branches are 100% bootstrap supported. B), feature frequency profiles (FFPs) tree. C), neighbor-joining tree based on the number of alleles that differ between any two strains. D), neighbor-joining tree based on the number of alleles that have none-zero DNA distance between any two strains. Unlike in C, small indels, including homopolymer sequencing errors, were not considered in D.</p>", "links"=>[], "tags"=>["phylogenies", "constructed", "125", "recombination"], "article_id"=>327811, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_E_coli_O104_H4_phylogenies_constructed_after_the_removal_of_the_125_gene_involved_in_recombination_in_ON2010_/327811", "title"=>"<i>E. coli</i> O104:H4 phylogenies constructed after the removal of the 125 gene involved in recombination in ON2010.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:10:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/657414"], "description"=>"<p>Only informative sites are shown with coordinates at the top. Sequences that are identical with the ON2010 sequence are highlighted in light green.</p>", "links"=>[], "tags"=>["alignments"], "article_id"=>327900, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_alignments_of_yaaH_A_and_EC55989_4986_B_/327900", "title"=>"Sequence alignments of <i>yaaH</i> (A) and <i>EC55989_4986</i> (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:11:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/657532"], "description"=>"<p>Regions that are identical with the ON2010 sequence are highlighted in light green.</p>", "links"=>[], "tags"=>["alignments"], "article_id"=>328021, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_alignments_of_the_araC_gene_/328021", "title"=>"Sequence alignments of the <i>araC</i> gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:13:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/657635"], "description"=>"<p>The data are plotted as of the gene order on the 55989 chromosome.</p>", "links"=>[], "tags"=>["on2011", "55989"], "article_id"=>328117, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.g011"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DNA_distance_between_ON2011_vs_55989_and_between_ON2011_and_01_09591_/328117", "title"=>"DNA distance between ON2011 vs. 55989 and between ON2011 and 01-09591.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:15:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/657692"], "description"=>"<p>When identical distance was observed in different groups for a gene, the nearest neighbor was assigned to the group most closely related to the B1 group.</p>", "links"=>[], "tags"=>["nearest", "neighbors", "125", "putative", "recombinant", "genes", "on2010"], "article_id"=>328170, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_nearest_neighbors_of_the_125_putative_recombinant_genes_in_the_ON2010_strain_/328170", "title"=>"Distribution of the nearest neighbors of the 125 putative recombinant genes in the ON2010 strain.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:16:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/657731"], "description"=>"<p>Differences between the plasmids in the ON2010 and 55989 strains.</p>", "links"=>[], "tags"=>["plasmids", "on2010", "55989"], "article_id"=>328214, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Weilong Hao", "Vanessa G. Allen", "Frances B. Jamieson", "Donald E. Low", "David C. Alexander"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033971.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differences_between_the_plasmids_in_the_ON2010_and_55989_strains_/328214", "title"=>"Differences between the plasmids in the ON2010 and 55989 strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:16:54"}

PMC Usage Stats | Further Information

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