Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak
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{"title"=>"Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak", "type"=>"journal", "authors"=>[{"first_name"=>"Midori", "last_name"=>"Kato-Maeda", "scopus_author_id"=>"6602111474"}, {"first_name"=>"Christine", "last_name"=>"Ho", "scopus_author_id"=>"7404653689"}, {"first_name"=>"Ben", "last_name"=>"Passarelli", "scopus_author_id"=>"51261425600"}, {"first_name"=>"Niaz", "last_name"=>"Banaei", "scopus_author_id"=>"24512294500"}, {"first_name"=>"Jennifer", "last_name"=>"Grinsdale", "scopus_author_id"=>"12785766500"}, {"first_name"=>"Laura", "last_name"=>"Flores", "scopus_author_id"=>"7101922951"}, {"first_name"=>"Jillian", "last_name"=>"Anderson", "scopus_author_id"=>"56654637300"}, {"first_name"=>"Megan", "last_name"=>"Murray", "scopus_author_id"=>"35479179200"}, {"first_name"=>"Graham", "last_name"=>"Rose", "scopus_author_id"=>"35410325200"}, {"first_name"=>"L. Masae", "last_name"=>"Kawamura", "scopus_author_id"=>"8922413300"}, {"first_name"=>"Nader", "last_name"=>"Pourmand", "scopus_author_id"=>"6602846511"}, {"first_name"=>"Muhammad A.", "last_name"=>"Tariq", "scopus_author_id"=>"7102752751"}, {"first_name"=>"Sebastien", "last_name"=>"Gagneux", "scopus_author_id"=>"6602524095"}, {"first_name"=>"Philip C.", "last_name"=>"Hopewell", "scopus_author_id"=>"24372908500"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"368465612", "pmid"=>"23472164", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0058235", "sgr"=>"84874625116", "scopus"=>"2-s2.0-84874625116"}, "id"=>"7b78e96d-9384-30ba-8048-d37d39d5b5c8", "abstract"=>"RATIONALE: Current tools available to study the molecular epidemiology of tuberculosis do not provide information about the directionality and sequence of transmission for tuberculosis cases occurring over a short period of time, such as during an outbreak. Recently, whole genome sequencing has been used to study molecular epidemiology of Mycobacterium tuberculosis over short time periods.\\n\\nOBJECTIVE: To describe the microevolution of M. tuberculosis during an outbreak caused by one drug-susceptible strain. METHOD AND MEASUREMENTS: We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina's sequencing by synthesis technology. A custom program written in Python was used to determine single nucleotide polymorphisms which were confirmed by PCR product Sanger sequencing.\\n\\nMAIN RESULTS: We obtained an average of 95.7% (94.1-96.9%) coverage for each isolate and an average fold read depth of 73 (1 to 250). We found 7 single nucleotide polymorphisms among the 9 isolates. The single nucleotide polymorphisms data confirmed all except one known epidemiological link. The outbreak strain resulted in 5 bacterial variants originating from the index case A1 with 0-2 mutations per transmission event that resulted in a secondary case.\\n\\nCONCLUSIONS: Whole genome sequencing analysis from a recent outbreak of tuberculosis enabled us to identify microevolutionary events observable during transmission, to determine 0-2 single nucleotide polymorphisms per transmission event that resulted in a secondary case, and to identify new epidemiologic links in the chain of transmission.", "link"=>"http://www.mendeley.com/research/whole-genome-sequencing-determine-microevolution-mycobacterium-tuberculosis-during-outbreak", "reader_count"=>134, "reader_count_by_academic_status"=>{"Unspecified"=>6, "Professor > Associate Professor"=>1, "Librarian"=>2, "Researcher"=>44, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>6, "Student > Master"=>30, "Other"=>3, "Student > Bachelor"=>10, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>6, "Professor > Associate Professor"=>1, "Librarian"=>2, "Researcher"=>44, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>6, "Student > Master"=>30, "Other"=>3, "Student > Bachelor"=>10, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Biochemistry, Genetics and Molecular Biology"=>23, "Mathematics"=>1, "Agricultural and Biological Sciences"=>61, "Medicine and Dentistry"=>24, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Chemistry"=>3, "Psychology"=>1, "Social Sciences"=>2, "Immunology and Microbiology"=>8}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>24}, "Chemistry"=>{"Chemistry"=>3}, "Social Sciences"=>{"Social Sciences"=>2}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>61}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>23}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>8}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "Colombia"=>1, "Sweden"=>1, "Belgium"=>2, "United States"=>3, "Rwanda"=>1, "United Kingdom"=>3, "Italy"=>2, "Zimbabwe"=>1, "Chile"=>1, "Spain"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/977691"], "description"=>"<p>The epidemiological links are shown with arrows. *Chest radiograph showing cavitation. †Positive sputum smear examination. ‡Laryngeal tuberculosis.</p>", "links"=>[], "tags"=>["patients"], "article_id"=>644815, "categories"=>["Microbiology", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Midori Kato-Maeda", "Christine Ho", "Ben Passarelli", "Niaz Banaei", "Jennifer Grinsdale", "Laura Flores", "Jillian Anderson", "Megan Murray", "Graham Rose", "L. Masae Kawamura", "Nader Pourmand", "Muhammad A. Tariq", "Sebastien Gagneux", "Philip C. Hopewell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058235.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Timeline_months_and_characteristics_of_the_patients_involved_in_the_outbreak_/644815", "title"=>"Timeline (months) and characteristics of the patients involved in the outbreak.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-06 09:11:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/977692"], "description"=>"<p>The letters inside the circles correspond to the patients; SNP correspond to the number of the SNP observed in the <i>M. tuberculosis</i> isolate and described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058235#pone-0058235-t001\" target=\"_blank\">Table 1</a>; lines represent links based on the SNPs and arrows show the sequential SNP acquisition. WT refers to the genotype of A1. *Mutations predicted to affect the protein according to SIFT. †Culture negative or not performed.</p>", "links"=>[], "tags"=>["public health and epidemiology", "Infectious diseases", "microbiology", "Computational biology", "Evolutionary biology"], "article_id"=>644816, "categories"=>["Microbiology", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Midori Kato-Maeda", "Christine Ho", "Ben Passarelli", "Niaz Banaei", "Jennifer Grinsdale", "Laura Flores", "Jillian Anderson", "Megan Murray", "Graham Rose", "L. Masae Kawamura", "Nader Pourmand", "Muhammad A. Tariq", "Sebastien Gagneux", "Philip C. Hopewell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058235.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNP_based_network_/644816", "title"=>"SNP-based network.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-06 09:12:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/977696", "https://ndownloader.figshare.com/files/977697"], "description"=>"<div><p>Rationale</p><p>Current tools available to study the molecular epidemiology of tuberculosis do not provide information about the directionality and sequence of transmission for tuberculosis cases occurring over a short period of time, such as during an outbreak. Recently, whole genome sequencing has been used to study molecular epidemiology of <i>Mycobacterium tuberculosis</i> over short time periods.</p> <p>Objective</p><p>To describe the microevolution of <i>M. tuberculosis</i> during an outbreak caused by one drug-susceptible strain.</p> <p>Method and Measurements</p><p>We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina’s sequencing by synthesis technology. A custom program written in Python was used to determine single nucleotide polymorphisms which were confirmed by PCR product Sanger sequencing.</p> <p>Main results</p><p>We obtained an average of 95.7% (94.1–96.9%) coverage for each isolate and an average fold read depth of 73 (1 to 250). We found 7 single nucleotide polymorphisms among the 9 isolates. The single nucleotide polymorphisms data confirmed all except one known epidemiological link. The outbreak strain resulted in 5 bacterial variants originating from the index case A1 with 0–2 mutations per transmission event that resulted in a secondary case.</p> <p>Conclusions</p><p>Whole genome sequencing analysis from a recent outbreak of tuberculosis enabled us to identify microevolutionary events observable during transmission, to determine 0–2 single nucleotide polymorphisms per transmission event that resulted in a secondary case, and to identify new epidemiologic links in the chain of transmission.</p> </div>", "links"=>[], "tags"=>["genome", "sequencing", "microevolution", "outbreak"], "article_id"=>644818, "categories"=>["Microbiology", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Midori Kato-Maeda", "Christine Ho", "Ben Passarelli", "Niaz Banaei", "Jennifer Grinsdale", "Laura Flores", "Jillian Anderson", "Megan Murray", "Graham Rose", "L. Masae Kawamura", "Nader Pourmand", "Muhammad A. Tariq", "Sebastien Gagneux", "Philip C. Hopewell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058235.s001", "https://dx.doi.org/10.1371/journal.pone.0058235.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Use_of_Whole_Genome_Sequencing_to_Determine_the_Microevolution_of_Mycobacterium_tuberculosis_during_an_Outbreak__/644818", "title"=>"Use of Whole Genome Sequencing to Determine the Microevolution of <em>Mycobacterium tuberculosis</em> during an Outbreak", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-06 09:12:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1006177"], "description"=>"*<p>By Himar1-based transposon mutagenesis in H37Rv strain culture in vitro <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058235#pone.0058235-Sassetti1\" target=\"_blank\">[27]</a>.</p>†<p>The first value is based on the SIFT prediction using the 13 non-<i>M. tuberculosis</i> complex genomes and the second value is based on the SWISS-PROT & TrEMBL sequence database.</p>", "links"=>[], "tags"=>["snps", "observed"], "article_id"=>666795, "categories"=>["Microbiology", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Midori Kato-Maeda", "Christine Ho", "Ben Passarelli", "Niaz Banaei", "Jennifer Grinsdale", "Laura Flores", "Jillian Anderson", "Megan Murray", "Graham Rose", "L. Masae Kawamura", "Nader Pourmand", "Muhammad A. Tariq", "Sebastien Gagneux", "Philip C. Hopewell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058235.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_SNPs_observed_among_the_nine_M_tuberculosis_isolates_/666795", "title"=>"Characteristics of the SNPs observed among the nine <i>M. tuberculosis</i> isolates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-05 01:53:15"}

PMC Usage Stats | Further Information

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Relative Metric

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