Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules
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{"title"=>"Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules", "type"=>"journal", "authors"=>[{"first_name"=>"Kalliopi", "last_name"=>"Georgiades", "scopus_author_id"=>"37003668900"}, {"first_name"=>"Didier", "last_name"=>"Raoult", "scopus_author_id"=>"36040059800"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"361467874", "doi"=>"10.1371/journal.pone.0017962", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"21437250", "issn"=>"19326203", "scopus"=>"2-s2.0-79952808907", "sgr"=>"79952808907"}, "id"=>"0f45ba5a-1fd0-3f00-8114-14eec0c431b7", "abstract"=>"BACKGROUND: We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans (\"bad bugs\") to their closest non-epidemic related species (\"controls\").\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We found several significantly different features in the \"bad bugs\", one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the \"bad bugs\", which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five \"bad bugs\" showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The \"bad bugs\" had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the \"bad bugs\" had surprisingly more toxin-antitoxin modules than did the controls.\\n\\nCONCLUSIONS/SIGNIFICANCE: We conclude that pathogenic capacity is not the result of \"virulence factors\" but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution.", "link"=>"http://www.mendeley.com/research/genomes-most-dangerous-epidemic-bacteria-virulence-repertoire-characterized-fewer-genes-more-toxinan", "reader_count"=>96, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>5, "Researcher"=>21, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>13, "Student > Bachelor"=>11, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>5, "Researcher"=>21, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>13, "Student > Bachelor"=>11, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Biochemistry, Genetics and Molecular Biology"=>14, "Mathematics"=>1, "Agricultural and Biological Sciences"=>64, "Medicine and Dentistry"=>2, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>3, "Engineering"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>64}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>8}}, "reader_count_by_country"=>{"Sweden"=>2, "United States"=>2, "Poland"=>1, "Italy"=>1, "Malaysia"=>1, "Chile"=>2, "France"=>1, "Spain"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/395387", "https://ndownloader.figshare.com/files/395466", "https://ndownloader.figshare.com/files/395550"], "description"=>"<div><h3>Background</h3><p>We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans (“bad bugs”) to their closest non-epidemic related species (“controls”).</p> <h3>Methodology/Principal Findings</h3><p>We found several significantly different features in the “bad bugs”, one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the “bad bugs”, which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five “bad bugs” showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The “bad bugs” had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the “bad bugs” had surprisingly more toxin-antitoxin modules than did the controls.</p> <h3>Conclusions/Significance</h3><p>We conclude that pathogenic capacity is not the result of “virulence factors” but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution.</p> </div>", "links"=>[], "tags"=>["genomes", "virulence", "repertoire", "characterized", "genes", "toxin-antitoxin", "modules"], "article_id"=>138113, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Kalliopi Georgiades", "Didier Raoult"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017962.s001", "https://dx.doi.org/10.1371/journal.pone.0017962.s002", "https://dx.doi.org/10.1371/journal.pone.0017962.s003"], "stats"=>{"downloads"=>8, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomes_of_the_Most_Dangerous_Epidemic_Bacteria_Have_a_Virulence_Repertoire_Characterized_by_Fewer_Genes_but_More_Toxin_Antitoxin_Modules/138113", "title"=>"Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-03-18 02:15:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/789808"], "description"=>"<p>A. Toxin-antitoxin systems (TA) characterize “bad bugs”. B. Bacterial character (“bad bugs”/controls) according to the TA content. The red dots representing the “bad bugs” are positioned separately from the blue dots representing the controls.</p>", "links"=>[], "tags"=>["11", "genomic"], "article_id"=>460178, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Kalliopi Georgiades", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017962.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_Component_Analysis_of_11_genomic_characteristics_/460178", "title"=>"Principal Component Analysis of 11 genomic characteristics.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-18 00:02:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/790224"], "description"=>"<p>Twelve bacterial couples and their genomic characteristics.</p>", "links"=>[], "tags"=>["bacterial", "couples", "genomic"], "article_id"=>460595, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Kalliopi Georgiades", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017962.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Twelve_bacterial_couples_and_their_genomic_characteristics_/460595", "title"=>"Twelve bacterial couples and their genomic characteristics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-18 00:09:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/790079"], "description"=>"<p>The circles with various colors represent different bacteria; the small brown circles represent the gene repertoire; the arrows around the bacteria represent gene exchange; the leaf, mouth and lungs represent the different potential niches colonized by a species. The red circle is a hyperspecialized bacterium with a decreased gene repertoire <i>via</i> gene loss.</p>", "links"=>[], "tags"=>["pathogenic"], "article_id"=>460457, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Kalliopi Georgiades", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017962.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hyperspecialized_pathogenic_species_evolution_/460457", "title"=>"Hyperspecialized pathogenic species evolution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-18 00:07:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/790197"], "description"=>"<p>Five bad bugs (*) have more poly (A) tails than their controls in number and percentage. The difference is statistically significant (p = 0.0001).</p>", "links"=>[], "tags"=>["poly", "tails"], "article_id"=>460570, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Kalliopi Georgiades", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017962.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_and_percentage_of_poly_A_tails_in_all_bacteria_used_/460570", "title"=>"Number and percentage of poly (A) tails in all bacteria used.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-18 00:09:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/789960"], "description"=>"<p>The “bad bugs” lack recombinational repair genes, whereas the controls lack mismatch excision repair genes.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Computational biology", "Evolutionary biology"], "article_id"=>460332, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Kalliopi Georgiades", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017962.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recombination_and_repair_genes_/460332", "title"=>"Recombination and repair genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-18 00:05:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/790165"], "description"=>"<p>Seven “bad bugs” (*) have more TA than “controls”. The difference was statistically significant (p = 0. 043).</p>", "links"=>[], "tags"=>["toxin-antitoxin", "24"], "article_id"=>460541, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Kalliopi Georgiades", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017962.t003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_toxin_antitoxin_in_each_of_the_seven_known_toxin_antitoxin_families_for_the_24_analyzed_genomes_/460541", "title"=>"Number of toxin-antitoxin in each of the seven known toxin-antitoxin families for the 24 analyzed genomes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-18 00:09:01"}

PMC Usage Stats | Further Information

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Relative Metric

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