Sequence Diversities of Serine-Aspartate Repeat Genes among Staphylococcus aureus Isolates from Different Hosts Presumably by Horizontal Gene Transfer
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{"title"=>"Sequence diversities of serine-aspartate repeat genes among staphylococcus aureus isolates from different hosts presumably by horizontal gene transfer", "type"=>"journal", "authors"=>[{"first_name"=>"Huping", "last_name"=>"Xue", "scopus_author_id"=>"36060592200"}, {"first_name"=>"Hong", "last_name"=>"Lu", "scopus_author_id"=>"37102004900"}, {"first_name"=>"Xin", "last_name"=>"Zhao", "scopus_author_id"=>"7407576254"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203", "pui"=>"361803757", "issn"=>"19326203", "pmid"=>"21625460", "doi"=>"10.1371/journal.pone.0020332", "sgr"=>"79956319737", "scopus"=>"2-s2.0-79956319737"}, "id"=>"5fc535fb-edf1-3834-8c59-b5e5798ba642", "abstract"=>"BACKGROUND: Horizontal gene transfer (HGT) is recognized as one of the major forces for bacterial genome evolution. Many clinically important bacteria may acquire virulence factors and antibiotic resistance through HGT. The comparative genomic analysis has become an important tool for identifying HGT in emerging pathogens. In this study, the Serine-Aspartate Repeat (Sdr) family has been compared among different sources of Staphylococcus aureus (S. aureus) to discover sequence diversities within their genomes. METHODOLOGY/PRINCIPAL FINDINGS: Four sdr genes were analyzed for 21 different S. aureus strains and 218 mastitis-associated S. aureus isolates from Canada. Comparative genomic analyses revealed that S. aureus strains from bovine mastitis (RF122 and mastitis isolates in this study), ovine mastitis (ED133), pig (ST398), chicken (ED98), and human methicillin-resistant S. aureus (MRSA) (TCH130, MRSA252, Mu3, Mu50, N315, 04-02981, JH1 and JH9) were highly associated with one another, presumably due to HGT. In addition, several types of insertion and deletion were found in sdr genes of many isolates. A new insertion sequence was found in mastitis isolates, which was presumably responsible for the HGT of sdrC gene among different strains. Moreover, the sdr genes could be used to type S. aureus. Regional difference of sdr genes distribution was also indicated among the tested S. aureus isolates. Finally, certain associations were found between sdr genes and subclinical or clinical mastitis isolates. CONCLUSIONS: Certain sdr gene sequences were shared in S. aureus strains and isolates from different species presumably due to HGT. Our results also suggest that the distributional assay of virulence factors should detect the full sequences or full functional regions of these factors. The traditional assay using short conserved regions may not be accurate or credible. These findings have important implications with regard to animal husbandry practices that may inadvertently enhance the contact of human and animal bacterial pathogens.", "link"=>"http://www.mendeley.com/research/sequence-diversities-serineaspartate-repeat-genes-among-staphylococcus-aureus-isolates-different-hos", "reader_count"=>26, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>4, "Student > Master"=>1, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>4, "Student > Master"=>1, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>15, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Social Sciences"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Denmark"=>1, "United Kingdom"=>1, "Portugal"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/773247"], "description"=>"<p>Alignment of a partial DNA sequence of <i>sdrC</i> gene of bovine mastitis isolates classifies <i>S. aureus</i> isolates. The same classification can be obtained by alignment of the full sequence of <i>sdrC</i> gene, as shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020332#pone.0020332.s001\" target=\"_blank\">Figure S1</a>. sdrC_CQ, sdrC_CE, sdrC_CO and sdrC_CW represent <i>sdrC</i> genes from clinical isolates of Quebec, Eastern Canada, Ontario and Western Canada, respectively. sdrC_Q, sdrC_E, sdrC_O and sdrC_W represent <i>sdrC</i> genes from subclinical isolates of Quebec, Eastern Canada, Ontario and Western Canada, respectively. <i>sdrC<sub>Q&E</sub></i> and <i>sdrC<sub>O&W</sub></i> stand for two different types of <i>sdrC</i> gene in isolates from the Quebec and Eastern Canada region, and from the Ontario and Western Canada region, respectively.</p>", "links"=>[], "tags"=>["mastitis-associated", "isolates", "was", "classified"], "article_id"=>443620, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Huping Xue", "Hong Lu", "Xin Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020332.g002", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bovine_mastitis_associated_S_aureus_isolates_was_classified_according_to_sdr_genes_/443620", "title"=>"Bovine mastitis-associated <i>S. aureus</i> isolates was classified according to <i>sdr</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-20 01:00:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/773415"], "description"=>"<p>The graph was constructed by using MEGA software (version 4.0) with the NJ method and bootstrap values were provided as percents over 1000 replications. Alignment gaps were considered complete deletion. A) Phylogenetic tree of <i>sdrC</i> gene. Q&E represents the isolates from Quebec and Eastern Canada; O&W represents the isolates from Ontario and Western Canada. B) Phylogenetic trees of <i>sdrD, sdrE</i> and <i>sdrH</i> genes. Canada in the <i>sdrD</i> phylogenetic tree denotes the isolates from all four Canadian regions.</p>", "links"=>[], "tags"=>["trees", "genes", "revealed", "evolutional", "aureus"], "article_id"=>443781, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Huping Xue", "Hong Lu", "Xin Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020332.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_trees_of_sdr_genes_revealed_the_evolutional_relationship_among_S_aureus_strains_and_isolates_/443781", "title"=>"Phylogenetic trees of <i>sdr</i> genes revealed the evolutional relationship among <i>S. aureus strains</i> and isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-20 01:03:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/773616"], "description"=>"<p>*Nucleotide numbers of the A region and B repeats of <i>sdrC, sdrD</i> and <i>sdrE</i> and the full sequence of <i>sdrH</i> in bovine mastitis isolates.</p>", "links"=>[], "tags"=>["identities", "genes", "isolates", "canada", "sequenced"], "article_id"=>443990, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Huping Xue", "Hong Lu", "Xin Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020332.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DNA_sequence_identities_of_sdr_genes_between_S_aureus_isolates_in_Canada_and_sequenced_S_aureus_strains_/443990", "title"=>"DNA sequence identities (%) of <i>sdr</i> genes between <i>S. aureus</i> isolates in Canada and sequenced <i>S. aureus</i> strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-20 01:06:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/773103"], "description"=>"<p>S represents the signal sequence while A and A' regions stand for putative ligand-binding A region. B1, B2, B3, B4, B5, B1′ and B2′ designate single B repeat. A'N and A'C are flanking regions of the insertion sequence which are identical to the N-terminus and the C-terminus of SdrC_ED133 A region, respectively; IS denotes an insertion sequence in the A region of SdrC_ED133; sdrH-N and sdrH-C represent flanking regions of the 3 repeats insertion sequence which are identical with N-terminus and the C-terminus of SdrH_O&W; IS' represents 3x repeats insertion sequence in sdrH mutant. 102 and 161 are the locations for the insertion. SdrC_Q&E represent the normal SdrC proteins in isolates from Quebec and East Canada; SdrC_mutant1 represents the insertion sequence found in SdrC in Canadian isolates E48, E49 and E50. SdrC_mutant2 represents the deletion sequence found in SdrC in Canadian isolates E5-16, CE6-14, CE16 and CE18; SdrD represents the normal SdrD proteins in Canadian isolates; SdrD_mutant represents the deletion sequence found in SdrD in Canadian isolates Q14, Q17, E7, E13, E21-24, E28-30, E45, E48, CE6-10, CE13, CE16, CE18-23, CE28, O3, O4, O18-20, CO4, CO7, CO8, CO11, CO16, CO18, CO20, O3, O4, O18-20, W9, W13, W15, W16, W20-23, W25, W32, W33, W35-37, W39, W40, CW3, CW4 and CW18; SdrH_O&W represents the normal SdrH proteins in isolates from Ontario and Western Canada; SdrH_mutant represents the insertion sequence found in SdrH in Ontario and Western Canada isolates O21-24.</p>", "links"=>[], "tags"=>["deletion", "mutations", "genes", "bovine", "mastitis-associated"], "article_id"=>443469, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Huping Xue", "Hong Lu", "Xin Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020332.g001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Insertion_and_deletion_mutations_in_sdr_genes_of_bovine_mastitis_associated_S_aureus_/443469", "title"=>"Insertion and deletion mutations in <i>sdr</i> genes of bovine mastitis-associated <i>S. aureus.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-20 00:57:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/773650"], "description"=>"<p>Primers used in PCR amplification of DNA sequence.</p>", "links"=>[], "tags"=>["pcr", "amplification", "dna"], "article_id"=>444022, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Huping Xue", "Hong Lu", "Xin Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020332.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_in_PCR_amplification_of_DNA_sequence_/444022", "title"=>"Primers used in PCR amplification of DNA sequence.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-20 01:07:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/773560"], "description"=>"<p>*CW, CO, CQ and CE represent clinical isolates from Western Canada, Ontario, Quebec and Eastern Canada, respectively. W, O, Q and E represent subclinical isolates from Western Canada, Ontario, Quebec and Eastern Canada, respectively.</p>", "links"=>[], "tags"=>["genes", "subclinical", "isolates", "bovine", "mastitis", "canadian"], "article_id"=>443927, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Huping Xue", "Hong Lu", "Xin Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020332.t002", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_sdr_genes_from_clinical_and_subclinical_isolates_of_bovine_mastitis_from_different_Canadian_regions_/443927", "title"=>"Distribution of <i>sdr</i> genes from clinical and subclinical isolates of bovine mastitis from different Canadian regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-20 01:05:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/388275", "https://ndownloader.figshare.com/files/388319"], "description"=>"<div><h3>Background</h3><p>Horizontal gene transfer (HGT) is recognized as one of the major forces for bacterial genome evolution. Many clinically important bacteria may acquire virulence factors and antibiotic resistance through HGT. The comparative genomic analysis has become an important tool for identifying HGT in emerging pathogens. In this study, the Serine-Aspartate Repeat (Sdr) family has been compared among different sources of <em>Staphylococcus aureus</em> (<em>S. aureus</em>) to discover sequence diversities within their genomes.</p> <h3>Methodology/Principal Findings</h3><p>Four <em>sdr</em> genes were analyzed for 21 different <em>S. aureus</em> strains and 218 mastitis-associated <em>S. aureus</em> isolates from Canada. Comparative genomic analyses revealed that <em>S. aureus</em> strains from bovine mastitis (RF122 and mastitis isolates in this study), ovine mastitis (ED133), pig (ST398), chicken (ED98), and human methicillin-resistant <em>S. aureus</em> (MRSA) (TCH130, MRSA252, Mu3, Mu50, N315, 04-02981, JH1 and JH9) were highly associated with one another, presumably due to HGT. In addition, several types of insertion and deletion were found in <em>sdr</em> genes of many isolates. A new insertion sequence was found in mastitis isolates, which was presumably responsible for the HGT of <em>sdrC</em> gene among different strains. Moreover, the <em>sdr</em> genes could be used to type <em>S. aureus.</em> Regional difference of <em>sdr</em> genes distribution was also indicated among the tested <em>S. aureus</em> isolates. Finally, certain associations were found between <em>sdr</em> genes and subclinical or clinical mastitis isolates.</p> <h3>Conclusions</h3><p>Certain <em>sdr</em> gene sequences were shared in <em>S. aureus</em> strains and isolates from different species presumably due to HGT. Our results also suggest that the distributional assay of virulence factors should detect the full sequences or full functional regions of these factors. The traditional assay using short conserved regions may not be accurate or credible. These findings have important implications with regard to animal husbandry practices that may inadvertently enhance the contact of human and animal bacterial pathogens.</p> </div>", "links"=>[], "tags"=>["diversities", "serine-aspartate", "genes", "isolates", "hosts", "horizontal"], "article_id"=>136676, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Huping Xue", "Hong Lu", "Xin Zhao"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0020332.s001", "https://dx.doi.org/10.1371/journal.pone.0020332.s002"], "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sequence_Diversities_of_Serine_Aspartate_Repeat_Genes_among_Staphylococcus_aureus_Isolates_from_Different_Hosts_Presumably_by_Horizontal_Gene_Transfer/136676", "title"=>"Sequence Diversities of Serine-Aspartate Repeat Genes among <em>Staphylococcus aureus</em> Isolates from Different Hosts Presumably by Horizontal Gene Transfer", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-05-20 01:51:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/773585"], "description"=>"<p>*MLST represents multilocus sequence typing.</p><p>**HA-MRSA means hospital-acquired methicillin-resistant <i>S. aureus</i>; CA-MSSA is the community-acquired methicillin-sensitive <i>S. aureus</i>; VISA is vancomycin-intermediate level-resistant <i>S. aureus</i>; VSSA represents vancomycin sensitive <i>S. aureus</i>.</p><p>***N/A, Not available.</p>", "links"=>[], "tags"=>["strains", "evaluated"], "article_id"=>443962, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Huping Xue", "Hong Lu", "Xin Zhao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020332.t003", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_S_aureus_strains_evaluated_in_this_study_/443962", "title"=>"<i>S. aureus</i> strains evaluated in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-20 01:06:02"}

PMC Usage Stats | Further Information

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Relative Metric

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