Comparative Genomics of Bordetella pertussis Reveals Progressive Gene Loss in Finnish Strains
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{"title"=>"Comparative genomics of Bordetella pertussis reveals progressive gene loss in Finnish strains", "type"=>"journal", "authors"=>[{"first_name"=>"Eriikka", "last_name"=>"Heikkinen", "scopus_author_id"=>"23987333200"}, {"first_name"=>"Teemu", "last_name"=>"Kallonen", "scopus_author_id"=>"23987339200"}, {"first_name"=>"Lilli", "last_name"=>"Saarinen", "scopus_author_id"=>"57154447800"}, {"first_name"=>"Rolf", "last_name"=>"Sara", "scopus_author_id"=>"55335092600"}, {"first_name"=>"Audrey J.", "last_name"=>"King", "scopus_author_id"=>"7403373458"}, {"first_name"=>"Frits R.", "last_name"=>"Mool", "scopus_author_id"=>"23987354100"}, {"first_name"=>"Juhani T.", "last_name"=>"Soini", "scopus_author_id"=>"7003605648"}, {"first_name"=>"Jussi", "last_name"=>"Mertsola", "scopus_author_id"=>"7004911408"}, {"first_name"=>"Qiushui", "last_name"=>"He", "scopus_author_id"=>"7402117945"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "scopus"=>"2-s2.0-41249088760", "doi"=>"10.1371/journal.pone.0000904", "pui"=>"351445318", "issn"=>"19326203", "pmid"=>"17878939", "sgr"=>"41249088760"}, "id"=>"d65f9059-5ba5-3ab5-ad8b-add35b1c0439", "abstract"=>"BACKGROUND: Bordetella pertussis is a gram-negative bacterium that infects the human respiratory tract and causes pertussis or whooping cough. The disease has resurged in many countries including Finland where the whole-cell pertussis vaccine has been used for more than 50 years. Antigenic divergence has been observed between vaccine strains and clinical isolates in Finland. To better understand genome evolution in B. pertussis circulating in the immunized population, we developed an oligonucleotide-based microarray for comparative genomic analysis of Finnish strains isolated during the period of 50 years.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: The microarray consisted of 3,582 oligonucleotides (70-mer) and covered 94% of 3,816 ORFs of Tohama I, the strain of which the genome has been sequenced. Twenty isolates from 1953 to 2004 were studied together with two Finnish vaccine strains and two international reference strains. The isolates were selected according to their characteristics, e.g. the year and place of isolation and pulsed-field gel electrophoresis profiles. Genomic DNA of the tested strains, along with reference DNA of Tohama I strain, was labelled and hybridized. The absence of genes as established with microarrays, was confirmed by PCR. Compared with the Tohama I strain, Finnish isolates lost 7 (8.6 kb) to 49 (55.3 kb) genes, clustered in one to four distinct loci. The number of lost genes increased with time, and one third of lost genes had functions related to inorganic ion transport and metabolism, or energy production and conversion. All four loci of lost genes were flanked by the insertion sequence element IS481.\\n\\nCONCLUSION/SIGNIFICANCE: Our results showed that the progressive gene loss occurred in Finnish B. pertussis strains isolated during a period of 50 years and confirmed that B. pertussis is dynamic and is continuously evolving, suggesting that the bacterium may use gene loss as one strategy to adapt to highly immunized populations.", "link"=>"http://www.mendeley.com/research/comparative-genomics-bordetella-pertussis-reveals-progressive-gene-loss-finnish-strains", "reader_count"=>30, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>5, "Student > Bachelor"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>5, "Student > Bachelor"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>17, "Medicine and Dentistry"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Hungary"=>1, "Egypt"=>1, "Brazil"=>1, "France"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/944657"], "description"=>"<p>The mean of intensity (A) is plotted against log-transformed intensity ratio (M) of individual spots. Two distinct clusters of the genes are shown. The genes present in both reference and testing strains were centered on zero, and the genes lost in the testing strain formed a separate cluster defined by M-value<−2.</p>", "links"=>[], "tags"=>["microarray"], "article_id"=>615040, "categories"=>["Microbiology"], "users"=>["Eriikka Heikkinen", "Teemu Kallonen", "Lilli Saarinen", "Rolf Sara", "Audrey J. King", "Frits R. Mooi", "Juhani T. Soini", "Jussi Mertsola", "Qiushui He"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000904.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MA_plot_analysis_of_microarray_results_of_a_B_pertussis_clinical_strain_PRCB179_/615040", "title"=>"MA-plot analysis of microarray results of a <i>B. pertussis</i> clinical strain (PRCB179).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-09-19 01:24:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/944974"], "description"=>"<p>Range of the lost genes in loci 1–4 is BP0910A-BP0934, BP1135-BP1141, BP1948-BP1966, and BP2088-BP2103, respectively. (+) and (−) indicates presence or absence of the locus.</p>1.<p>International reference strain</p>2.<p>Three genes in the locus were lost (BP0910A-BP0912).</p>3.<p>Strain used for the production of whole cell vaccine in Finland since 1962 and obtained from USA.</p>4.<p>Strain added to the whole cell vaccine in 1976 and obtained from UK.</p>", "links"=>[], "tags"=>["bacterial", "strains", "absent", "genes"], "article_id"=>615341, "categories"=>["Microbiology"], "users"=>["Eriikka Heikkinen", "Teemu Kallonen", "Lilli Saarinen", "Rolf Sara", "Audrey J. King", "Frits R. Mooi", "Juhani T. Soini", "Jussi Mertsola", "Qiushui He"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000904.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_bacterial_strains_and_the_distribution_of_absent_genes_detected_by_microarray_/615341", "title"=>"Characteristics of the bacterial strains and the distribution of absent genes detected by microarray.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-09-19 01:29:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/465055", "https://ndownloader.figshare.com/files/465087", "https://ndownloader.figshare.com/files/465139"], "description"=>"<div><h3>Background</h3><p><em>Bordetella pertussis</em> is a Gram-negative bacterium that infects the human respiratory tract and causes pertussis or whooping cough. The disease has resurged in many countries including Finland where the whole-cell pertussis vaccine has been used for more than 50 years. Antigenic divergence has been observed between vaccine strains and clinical isolates in Finland. To better understand genome evolution in <em>B. pertussis</em> circulating in the immunized population, we developed an oligonucleotide-based microarray for comparative genomic analysis of Finnish strains isolated during the period of 50 years.</p><h3>Methodology/Principal Findings</h3><p>The microarray consisted of 3,582 oligonucleotides (70-mer) and covered 94% of 3,816 ORFs of Tohama I, the strain of which the genome has been sequenced <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000904#pone.0000904-Parkhill1\">[1]</a>. Twenty isolates from 1953 to 2004 were studied together with two Finnish vaccine strains and two international reference strains. The isolates were selected according to their characteristics, <em>e.g.</em> the year and place of isolation and pulsed-field gel electrophoresis profiles. Genomic DNA of the tested strains, along with reference DNA of Tohama I strain, was labelled and hybridized. The absence of genes as established with microarrays, was confirmed by PCR. Compared with the Tohama I strain, Finnish isolates lost 7 (8.6 kb) to 49 (55.3 kb) genes, clustered in one to four distinct loci. The number of lost genes increased with time, and one third of lost genes had functions related to inorganic ion transport and metabolism, or energy production and conversion. All four loci of lost genes were flanked by the insertion sequence element IS<em>481</em>.</p><h3>Conclusion/Significance</h3><p>Our results showed that the progressive gene loss occurred in Finnish <em>B. pertussis</em> strains isolated during a period of 50 years and confirmed that <em>B. pertussis</em> is dynamic and is continuously evolving, suggesting that the bacterium may use gene loss as one strategy to adapt to highly immunized populations.</p></div>", "links"=>[], "tags"=>["comparative", "genomics", "reveals", "finnish", "strains"], "article_id"=>151674, "categories"=>["Microbiology"], "users"=>["Eriikka Heikkinen", "Teemu Kallonen", "Lilli Saarinen", "Rolf Sara", "Audrey J. King", "Frits R. Mooi", "Juhani T. Soini", "Jussi Mertsola", "Qiushui He"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000904.s001", "https://dx.doi.org/10.1371/journal.pone.0000904.s002", "https://dx.doi.org/10.1371/journal.pone.0000904.s003"], "stats"=>{"downloads"=>5, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparative_Genomics_of_Bordetella_pertussis_Reveals_Progressive_Gene_Loss_in_Finnish_Strains/151674", "title"=>"Comparative Genomics of <em>Bordetella pertussis</em> Reveals Progressive Gene Loss in Finnish Strains", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-09-19 00:27:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/944938"], "description"=>"1.<p>No of duplicated genes defined in COG</p>", "links"=>[], "tags"=>["absent", "duplicated", "genes", "finnish", "strains", "genome", "tohama"], "article_id"=>615299, "categories"=>["Microbiology"], "users"=>["Eriikka Heikkinen", "Teemu Kallonen", "Lilli Saarinen", "Rolf Sara", "Audrey J. King", "Frits R. Mooi", "Juhani T. Soini", "Jussi Mertsola", "Qiushui He"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000904.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_absent_and_duplicated_genes_detected_in_Finnish_clinical_strains_and_vaccine_strain_and_the_reference_strain_relative_to_the_genome_of_B_pertussis_Tohama_I_/615299", "title"=>"Number of absent and duplicated genes detected in Finnish clinical strains and vaccine strain and the reference strain relative to the genome of <i>B. pertussis</i> Tohama I.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-09-19 01:28:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/944731"], "description"=>"<p>The DNA profiles obtained after restriction with XbaI are shown, and only different PFGE profiles identified among the strains tested by microarray were included. The unweighted pair group method using arithmetic averages (UPGMA) with 1% band tolerance and 1% optimization settings was used as the clustering method.</p>", "links"=>[], "tags"=>["pfge", "profiles"], "article_id"=>615115, "categories"=>["Microbiology"], "users"=>["Eriikka Heikkinen", "Teemu Kallonen", "Lilli Saarinen", "Rolf Sara", "Audrey J. King", "Frits R. Mooi", "Juhani T. Soini", "Jussi Mertsola", "Qiushui He"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000904.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dendrogram_analysis_of_PFGE_profiles_of_B_pertussis_clinical_and_reference_strains_/615115", "title"=>"Dendrogram analysis of PFGE profiles of <i>B. pertussis</i> clinical and reference strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-09-19 01:25:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/944826"], "description"=>"<p>Number of the genes is shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000904#pone-0000904-t002\" target=\"_blank\">Table 2</a>.</p>", "links"=>[], "tags"=>["duplicated", "genes", "defined", "20", "functions", "clusters", "orthologous"], "article_id"=>615191, "categories"=>["Microbiology"], "users"=>["Eriikka Heikkinen", "Teemu Kallonen", "Lilli Saarinen", "Rolf Sara", "Audrey J. King", "Frits R. Mooi", "Juhani T. Soini", "Jussi Mertsola", "Qiushui He"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000904.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distributions_of_lost_and_duplicated_genes_defined_in_the_20_functions_based_on_the_Clusters_of_Orthologous_Groups_/615191", "title"=>"Distributions of lost and duplicated genes defined in the 20 functions based on the Clusters of Orthologous Groups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-09-19 01:26:31"}

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Relative Metric

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