Multi Locus Sequence Typing of Chlamydia Reveals an Association between Chlamydia psittaci Genotypes and Host Species
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{"title"=>"Multi locus sequence typing of Chlamydia reveals an association between Chlamydia psittaci genotypes and host species", "type"=>"journal", "authors"=>[{"first_name"=>"Yvonne", "last_name"=>"Pannekoek", "scopus_author_id"=>"6602804891"}, {"first_name"=>"Veerle", "last_name"=>"Dickx", "scopus_author_id"=>"36489535600"}, {"first_name"=>"Delphine S.A.Beeckman", "last_name"=>"Beeckman", "scopus_author_id"=>"6602786732"}, {"first_name"=>"Keith A.", "last_name"=>"Jolley", "scopus_author_id"=>"7003265292"}, {"first_name"=>"Wendy C.", "last_name"=>"Keijzers", "scopus_author_id"=>"6507731684"}, {"first_name"=>"Evangelia", "last_name"=>"Vretou", "scopus_author_id"=>"6701623783"}, {"first_name"=>"Martin C.J.Maiden", "last_name"=>"Maiden", "scopus_author_id"=>"7006019693"}, {"first_name"=>"Daisy", "last_name"=>"Vanrompay", "scopus_author_id"=>"7004065189"}, {"first_name"=>"Arie", "last_name"=>"van der Ende", "scopus_author_id"=>"7007055960"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0014179", "sgr"=>"78649936336", "issn"=>"19326203", "pui"=>"360125626", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"21152037", "scopus"=>"2-s2.0-78649936336"}, "id"=>"022c63c5-e0da-3d44-94af-e82715a73239", "abstract"=>"Chlamydia comprises a group of obligate intracellular bacterial parasites responsible for a variety of diseases in humans and animals, including several zoonoses. Chlamydia trachomatis causes diseases such as trachoma, urogenital infection and lymphogranuloma venereum with severe morbidity. Chlamydia pneumoniae is a common cause of community-acquired respiratory tract infections. Chlamydia psittaci, causing zoonotic pneumonia in humans, is usually hosted by birds, while Chlamydia abortus, causing abortion and fetal death in mammals, including humans, is mainly hosted by goats and sheep. We used multi-locus sequence typing to asses the population structure of Chlamydia. In total, 132 Chlamydia isolates were analyzed, including 60 C. trachomatis, 18 C. pneumoniae, 16 C. abortus, 34 C. psittaci and one of each of C. pecorum, C. caviae, C. muridarum and C. felis. Cluster analyses utilizing the Neighbour-Joining algorithm with the maximum composite likelihood model of concatenated sequences of 7 housekeeping fragments showed that C. psittaci 84/2334 isolated from a parrot grouped together with the C. abortus isolates from goats and sheep. Cluster analyses of the individual alleles showed that in all instances C. psittaci 84/2334 formed one group with C. abortus. Moving 84/2334 from the C. psittaci group to the C. abortus group resulted in a significant increase in the number of fixed differences and elimination of the number of shared mutations between C. psittaci and C. abortus. C. psittaci M56 from a muskrat branched separately from the main group of C. psittaci isolates. C. psittaci genotypes appeared to be associated with host species. The phylogentic tree of C. psittaci did not follow that of its host bird species, suggesting host species jumps. In conclusion, we report for the first time an association between C. psittaci genotypes with host species.", "link"=>"http://www.mendeley.com/research/multi-locus-sequence-typing-chlamydia-reveals-association-between-chlamydia-psittaci-genotypes-host", "reader_count"=>42, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Materials Science"=>1, "Agricultural and Biological Sciences"=>18, "Medicine and Dentistry"=>8, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Psychology"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>18}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>4}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/814992"], "description"=>"<p>*d<sub>S</sub> and d<sub>N</sub>: the average number of synonymous substitutions per synonymous site and nonsynonymous substitutions per nonsynonymous site, respectively (Jukes-Cantor corrected).</p>", "links"=>[], "tags"=>["microbiology/medical microbiology", "microbiology/microbial evolution and genomics", "infectious diseases/bacterial infections"], "article_id"=>485356, "categories"=>["Infectious Diseases", "Microbiology"], "users"=>["Yvonne Pannekoek", "Veerle Dickx", "Delphine S. A. Beeckman", "Keith A. Jolley", "Wendy C. Keijzers", "Evangelia Vretou", "Martin C. J. Maiden", "Daisy Vanrompay", "Arie van der Ende"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014179.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_of_Chlamydia_/485356", "title"=>"Diversity of <i>Chlamydia</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-02 01:29:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/814819"], "description"=>"<p>Concatenated sequences were aligned and analysed in MEGA 4.0.2. Phylogenetic tree was constructed using the Neighbour-Joining algorithm using Maximum Composite Likelihood model. Bootstrap test was for 5000 repetitions. Numbers indicate bootstrap values over 50%. Only unique genotypes (STs) were included in the clustering analyses. STs are displayed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014179#pone.0014179.s001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["analyses", "concatenated", "sequences", "housekeeping", "fragments"], "article_id"=>485175, "categories"=>["Infectious Diseases", "Microbiology"], "users"=>["Yvonne Pannekoek", "Veerle Dickx", "Delphine S. A. Beeckman", "Keith A. Jolley", "Wendy C. Keijzers", "Evangelia Vretou", "Martin C. J. Maiden", "Daisy Vanrompay", "Arie van der Ende"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014179.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analyses_of_concatenated_sequences_of_7_housekeeping_gene_fragments_of_C_psittaci_and_C_abortus_strains_/485175", "title"=>"Phylogenetic analyses of concatenated sequences of 7 housekeeping gene fragments of <i>C. psittaci</i> and <i>C. abortus</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-02 01:26:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/406300", "https://ndownloader.figshare.com/files/406319", "https://ndownloader.figshare.com/files/406349"], "description"=>"<div><p><em>Chlamydia</em> comprises a group of obligate intracellular bacterial parasites responsible for a variety of diseases in humans and animals, including several zoonoses. <em>Chlamydia trachomatis</em> causes diseases such as trachoma, urogenital infection and lymphogranuloma venereum with severe morbidity. <em>Chlamydia pneumoniae</em> is a common cause of community-acquired respiratory tract infections. <em>Chlamydia psittaci</em>, causing zoonotic pneumonia in humans, is usually hosted by birds, while <em>Chlamydia abortus</em>, causing abortion and fetal death in mammals, including humans, is mainly hosted by goats and sheep. We used multi-locus sequence typing to asses the population structure of <em>Chlamydia</em>. In total, 132 <em>Chlamydia</em> isolates were analyzed, including 60 <em>C. trachomatis</em>, 18 <em>C. pneumoniae</em>, 16 <em>C. abortus</em>, 34 <em>C. psittaci</em> and one of each of <em>C. pecorum</em>, <em>C. caviae</em>, <em>C. muridarum</em> and <em>C. felis</em>. Cluster analyses utilizing the Neighbour-Joining algorithm with the maximum composite likelihood model of concatenated sequences of 7 housekeeping fragments showed that <em>C. psittaci</em> 84/2334 isolated from a parrot grouped together with the <em>C. abortus</em> isolates from goats and sheep. Cluster analyses of the individual alleles showed that in all instances <em>C. psittaci</em> 84/2334 formed one group with <em>C. abortus</em>. Moving 84/2334 from the <em>C. psittaci</em> group to the <em>C. abortus</em> group resulted in a significant increase in the number of fixed differences and elimination of the number of shared mutations between <em>C. psittaci</em> and <em>C. abortus</em>. <em>C. psittaci</em> M56 from a muskrat branched separately from the main group of <em>C. psittaci</em> isolates. <em>C. psittaci</em> genotypes appeared to be associated with host species. The phylogentic tree of <em>C. psittaci</em> did not follow that of its host bird species, suggesting host species jumps. In conclusion, we report for the first time an association between <em>C. psittaci</em> genotypes with host species.</p></div>", "links"=>[], "tags"=>["multi", "locus", "typing", "reveals", "genotypes"], "article_id"=>140273, "categories"=>["Cancer", "Microbiology"], "users"=>["Yvonne Pannekoek", "Veerle Dickx", "Delphine S. A. Beeckman", "Keith A. Jolley", "Wendy C. Keijzers", "Evangelia Vretou", "Martin C. J. Maiden", "Daisy Vanrompay", "Arie van der Ende"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0014179.s001", "https://dx.doi.org/10.1371/journal.pone.0014179.s002", "https://dx.doi.org/10.1371/journal.pone.0014179.s003"], "stats"=>{"downloads"=>12, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Multi_Locus_Sequence_Typing_of_Chlamydia_Reveals_an_Association_between_Chlamydia_psittaci_Genotypes_and_Host_Species/140273", "title"=>"Multi Locus Sequence Typing of <em>Chlamydia</em> Reveals an Association between <em>Chlamydia psittaci</em> Genotypes and Host Species", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-12-02 00:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/814910"], "description"=>"<p>Concatenated sequences were aligned and analysed in MEGA 4.0.2. Phylogenetic tree was constructed using the Neighbour-Joining algorithm using Maximum Composite Likelihood model. Bootstrap test was for 5000 repetitions. Numbers indicate bootstrap values over 50%.</p>", "links"=>[], "tags"=>["analyses", "concatenated", "sequences", "housekeeping", "fragments", "excluding"], "article_id"=>485258, "categories"=>["Infectious Diseases", "Microbiology"], "users"=>["Yvonne Pannekoek", "Veerle Dickx", "Delphine S. A. Beeckman", "Keith A. Jolley", "Wendy C. Keijzers", "Evangelia Vretou", "Martin C. J. Maiden", "Daisy Vanrompay", "Arie van der Ende"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014179.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analyses_of_concatenated_sequences_of_7_housekeeping_gene_fragments_of_C_psittaci_strains_excluding_strain_84_2334_and_M56_/485258", "title"=>"Phylogenetic analyses of concatenated sequences of 7 housekeeping gene fragments of <i>C. psittaci</i> strains, excluding strain 84/2334 and M56.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-02 01:27:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/815041"], "description"=>"<p>*D<sub>XY</sub>: Average number of nucleotide substitutions per site between populations (Jukes-Cantor corrected).</p>", "links"=>[], "tags"=>["microbiology/medical microbiology", "microbiology/microbial evolution and genomics", "infectious diseases/bacterial infections"], "article_id"=>485399, "categories"=>["Infectious Diseases", "Microbiology"], "users"=>["Yvonne Pannekoek", "Veerle Dickx", "Delphine S. A. Beeckman", "Keith A. Jolley", "Wendy C. Keijzers", "Evangelia Vretou", "Martin C. J. Maiden", "Daisy Vanrompay", "Arie van der Ende"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014179.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Divergence_between_Chlamydia_species_/485399", "title"=>"Divergence between <i>Chlamydia</i> species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-02 01:29:59"}

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