Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints
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{"title"=>"Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints", "type"=>"journal", "authors"=>[{"first_name"=>"Stefan", "last_name"=>"Niemann", "scopus_author_id"=>"7006827120"}, {"first_name"=>"Claudio U.", "last_name"=>"Köser", "scopus_author_id"=>"26023473900"}, {"first_name"=>"Sebastien", "last_name"=>"Gagneux", "scopus_author_id"=>"6602524095"}, {"first_name"=>"Claudia", "last_name"=>"Plinke", "scopus_author_id"=>"13405991700"}, {"first_name"=>"Susanne", "last_name"=>"Homolka", "scopus_author_id"=>"24461541400"}, {"first_name"=>"Helen", "last_name"=>"Bignell", "scopus_author_id"=>"25636817100"}, {"first_name"=>"Richard J.", "last_name"=>"Carter", "scopus_author_id"=>"57198722665"}, {"first_name"=>"R. Keira", "last_name"=>"Cheetham", "scopus_author_id"=>"35114541800"}, {"first_name"=>"Anthony", "last_name"=>"Cox", "scopus_author_id"=>"55271758300"}, {"first_name"=>"Niall A.", "last_name"=>"Gormley", "scopus_author_id"=>"36981047200"}, {"first_name"=>"Paula", "last_name"=>"Kokko-Gonzales", "scopus_author_id"=>"6504098822"}, {"first_name"=>"Lisa J.", "last_name"=>"Murray", "scopus_author_id"=>"18434745300"}, {"first_name"=>"Roberto", "last_name"=>"Rigatti", "scopus_author_id"=>"6506145151"}, {"first_name"=>"Vincent P.", "last_name"=>"Smith", "scopus_author_id"=>"57199437037"}, {"first_name"=>"Felix P.M.", "last_name"=>"Arends", "scopus_author_id"=>"35228570300"}, {"first_name"=>"Helen S.", "last_name"=>"Cox", "scopus_author_id"=>"35228720000"}, {"first_name"=>"Geoff", "last_name"=>"Smith", "scopus_author_id"=>"24375409300"}, {"first_name"=>"John A.C.", "last_name"=>"Archer", "scopus_author_id"=>"56701054100"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"355559695", "sgr"=>"70350719440", "doi"=>"10.1371/journal.pone.0007407", "scopus"=>"2-s2.0-70350719440", "pmid"=>"19823582"}, "id"=>"9c2a39bd-87e9-3a2b-93de-ae78c53cad7e", "abstract"=>"BACKGROUND: Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1) and one multidrug resistant (MDR) isolate (K-2) of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci. We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations.\\n\\nCONCLUSIONS: Our results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using standard genotyping tools if the overall diversity of circulating clones is limited. These findings have important implications for clinical trials of new anti-tuberculosis drugs.", "link"=>"http://www.mendeley.com/research/genomic-diversity-among-drug-sensitive-multidrug-resistant-isolates-mycobacterium-tuberculosis-ident", "reader_count"=>161, "reader_count_by_academic_status"=>{"Unspecified"=>9, "Professor > Associate Professor"=>6, "Librarian"=>1, "Researcher"=>38, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>38, "Student > Postgraduate"=>8, "Student > Master"=>32, "Other"=>4, "Student > Bachelor"=>11, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>9, "Professor > Associate Professor"=>6, "Librarian"=>1, "Researcher"=>38, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>38, "Student > Postgraduate"=>8, "Student > Master"=>32, "Other"=>4, "Student > Bachelor"=>11, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>15, "Agricultural and Biological Sciences"=>77, "Arts and Humanities"=>1, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Computer Science"=>3, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>20, "Materials Science"=>1, "Mathematics"=>1, "Medicine and Dentistry"=>29, "Physics and Astronomy"=>1, "Psychology"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>7}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>29}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>15}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>7}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>77}, "Computer Science"=>{"Computer Science"=>3}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>20}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>2, "Norway"=>1, "Philippines"=>1, "United Kingdom"=>2, "India"=>1, "Spain"=>1, "Russia"=>3}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/436642", "https://ndownloader.figshare.com/files/436797", "https://ndownloader.figshare.com/files/436819", "https://ndownloader.figshare.com/files/436847", "https://ndownloader.figshare.com/files/436864", "https://ndownloader.figshare.com/files/436876"], "description"=>"<div><h3>Background</h3><p><em>Mycobacterium tuberculosis</em> complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients.</p><h3>Methodology/Principal Findings</h3><p>Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1) and one multidrug resistant (MDR) isolate (K-2) of a rapidly spreading <em>M. tuberculosis</em> Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS<em>6110</em> RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci.</p><p>We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations.</p><h3>Conclusions</h3><p>Our results suggest that <em>M. tuberculosis</em> isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using standard genotyping tools if the overall diversity of circulating clones is limited. These findings have important implications for clinical trials of new anti-tuberculosis drugs.</p></div>", "links"=>[], "tags"=>["genomic", "multidrug", "resistant", "isolates", "dna", "fingerprints"], "article_id"=>146093, "categories"=>["Cancer", "Medicine", "Microbiology", "Genetics"], "users"=>["Stefan Niemann", "Claudio U. Köser", "Sebastien Gagneux", "Claudia Plinke", "Susanne Homolka", "Helen Bignell", "Richard J. Carter", "R. Keira Cheetham", "Anthony Cox", "Niall A. Gormley", "Paula Kokko-Gonzales", "Lisa J. Murray", "Roberto Rigatti", "Vincent P. Smith", "Felix P. M. Arends", "Helen S. Cox", "Geoff Smith", "John A. C. Archer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0007407.s001", "https://dx.doi.org/10.1371/journal.pone.0007407.s002", "https://dx.doi.org/10.1371/journal.pone.0007407.s003", "https://dx.doi.org/10.1371/journal.pone.0007407.s004", "https://dx.doi.org/10.1371/journal.pone.0007407.s005", "https://dx.doi.org/10.1371/journal.pone.0007407.s006"], "stats"=>{"downloads"=>14, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Diversity_among_Drug_Sensitive_and_Multidrug_Resistant_Isolates_of_Mycobacterium_tuberculosis_with_Identical_DNA_Fingerprints/146093", "title"=>"Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of <em>Mycobacterium tuberculosis</em> with Identical DNA Fingerprints", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-10-12 01:41:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/880099"], "description"=>"<p>A, Graph showing the depth of coverage. A drop in coverage is visible in K-1 suggesting a deletion relative to the H37Rv reference. B, PCR and subsequent dideoxy sequencing (data not shown) identified a K-1 specific deletion at 859244-859501 (257 bp) affecting <i>cyp123</i> (<i>Rv0766c</i>) in correspondence with the coverage plot (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone-0007407-g003\" target=\"_blank\">Figure 3A</a>).</p>", "links"=>[], "tags"=>["deletion"], "article_id"=>550540, "categories"=>["Infectious Diseases", "Medicine", "Microbiology", "Genetics", "Virology"], "users"=>["Stefan Niemann", "Claudio U. Köser", "Sebastien Gagneux", "Claudia Plinke", "Susanne Homolka", "Helen Bignell", "Richard J. Carter", "R. Keira Cheetham", "Anthony Cox", "Niall A. Gormley", "Paula Kokko-Gonzales", "Lisa J. Murray", "Roberto Rigatti", "Vincent P. Smith", "Felix P. M. Arends", "Helen S. Cox", "Geoff Smith", "John A. C. Archer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007407.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_deletion_specific_for_K_1_/550540", "title"=>"Genomic deletion specific for K-1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-12 00:09:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/880188"], "description"=>"<p>Edwards' Venn diagram showing the distribution of SNPs in K-1 (1,338 total) and the published genomes of CDC1551 (1,114 total), F11 (833 total) and <i>M. bovis</i> (2,294 total) relative to the published H37Rv sequence.</p>", "links"=>[], "tags"=>["snps", "mtb"], "article_id"=>550631, "categories"=>["Infectious Diseases", "Medicine", "Microbiology", "Genetics", "Virology"], "users"=>["Stefan Niemann", "Claudio U. Köser", "Sebastien Gagneux", "Claudia Plinke", "Susanne Homolka", "Helen Bignell", "Richard J. Carter", "R. Keira Cheetham", "Anthony Cox", "Niall A. Gormley", "Paula Kokko-Gonzales", "Lisa J. Murray", "Roberto Rigatti", "Vincent P. Smith", "Felix P. M. Arends", "Helen S. Cox", "Geoff Smith", "John A. C. Archer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007407.g004", "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_SNPs_across_Mtb_genomes_/550631", "title"=>"Comparison of SNPs across Mtb genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-12 00:10:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/880246"], "description"=>"a<p>Mutation leads to high level resistance.</p>b<p>Please note that this corresponds to amino acid 45<b><u>8</u></b> based on the TIGR annotation of H37Rv (<a href=\"http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?org=ntmt02\" target=\"_blank\">http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?org=ntmt02</a>) in which the N-terminus was annotated to start 6 amino acids upstream of the start in TubercuList. The equivalent amino acid in <i>E. coli</i> is 533.</p>c<p>For a detailed discussion of this mutation please refer to the Supplementary Results(<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone.0007407.s001\" target=\"_blank\">File S1</a>).</p>", "links"=>[], "tags"=>["k-2", "antibiotic"], "article_id"=>550691, "categories"=>["Infectious Diseases", "Medicine", "Microbiology", "Genetics", "Virology"], "users"=>["Stefan Niemann", "Claudio U. Köser", "Sebastien Gagneux", "Claudia Plinke", "Susanne Homolka", "Helen Bignell", "Richard J. Carter", "R. Keira Cheetham", "Anthony Cox", "Niall A. Gormley", "Paula Kokko-Gonzales", "Lisa J. Murray", "Roberto Rigatti", "Vincent P. Smith", "Felix P. M. Arends", "Helen S. Cox", "Geoff Smith", "John A. C. Archer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007407.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNPs_in_K_2_responsible_for_antibiotic_resistances_/550691", "title"=>"SNPs in K-2 responsible for antibiotic resistances.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-10-12 00:11:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/880305"], "description"=>"<p>Large chromosomal deletions detected in both Beijing isolates K-1 and K-2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone.0007407-Tsolaki1\" target=\"_blank\">[57]</a>.</p>", "links"=>[], "tags"=>["chromosomal", "deletions", "beijing", "isolates", "k-1", "k-2"], "article_id"=>550744, "categories"=>["Infectious Diseases", "Medicine", "Microbiology", "Genetics", "Virology"], "users"=>["Stefan Niemann", "Claudio U. Köser", "Sebastien Gagneux", "Claudia Plinke", "Susanne Homolka", "Helen Bignell", "Richard J. Carter", "R. Keira Cheetham", "Anthony Cox", "Niall A. Gormley", "Paula Kokko-Gonzales", "Lisa J. Murray", "Roberto Rigatti", "Vincent P. Smith", "Felix P. M. Arends", "Helen S. Cox", "Geoff Smith", "John A. C. Archer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007407.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Large_chromosomal_deletions_detected_in_both_Beijing_isolates_K_1_and_K_2_57_/550744", "title"=>"Large chromosomal deletions detected in both Beijing isolates K-1 and K-2 [57].", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-10-12 00:12:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/879995"], "description"=>"<p>A, Venn diagram showing the SNP distribution between the three genomes under investigation (H37Rv, K-1, and K-2) relative to the published H37Rv sequence. The 75 K-2 specific SNPs encompassed the 5 resistance conferring SNPs (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone-0007407-t002\" target=\"_blank\">Table 2</a>). 44 of the 74 SNPs shared in the three genomes were found to be errors in the H37Rv reference (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone.0007407.s001\" target=\"_blank\">File S1</a>). B, Summary of nature and location of SNPs detected in this study. C, Circular plot of H37Rv reference genome prepared with DNAPlotter <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone.0007407-Carver1\" target=\"_blank\">[46]</a>. The two outer-most circles show the genes on the forward and reverse strand respectively with the annotation and colour coding derived from TubercuList <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone.0007407-Cole2\" target=\"_blank\">[47]</a>. The remaining 5 internal circles correspond to the 5 filled subsection of the Venn diagram in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone-0007407-g002\" target=\"_blank\">Figure 2A</a> with identical colour coding (from third to inner-most circle: SNPs common to all 3 genomes; Beijing K-family backbone SNPs; K-1, K-2 and H37Rv specific SNPs). Non-synonymous or inter-genic SNPs are shown as long lines whereas short lines represent synonymous SNPs. In two cases, where a SNP was non-synonymous in one gene and synonymous in a second, overlapping gene intermediate lines were used. The 5 resistance causing mutations in K-2 (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone-0007407-t002\" target=\"_blank\">Table 2</a>) are highlighted separately in red on the outside. An equivalent, fully zoomable representation for each individual genome based on Artemis <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone.0007407-Rutherford1\" target=\"_blank\">[25]</a> is available in the Supplement (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone.0007407.s003\" target=\"_blank\">Files S3</a>-<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007407#pone.0007407.s006\" target=\"_blank\">S6</a>).</p>", "links"=>[], "tags"=>["genome"], "article_id"=>550437, "categories"=>["Infectious Diseases", "Medicine", "Microbiology", "Genetics", "Virology"], "users"=>["Stefan Niemann", "Claudio U. Köser", "Sebastien Gagneux", "Claudia Plinke", "Susanne Homolka", "Helen Bignell", "Richard J. Carter", "R. Keira Cheetham", "Anthony Cox", "Niall A. Gormley", "Paula Kokko-Gonzales", "Lisa J. Murray", "Roberto Rigatti", "Vincent P. Smith", "Felix P. M. Arends", "Helen S. Cox", "Geoff Smith", "John A. C. Archer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007407.g002", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_genome_data_obtained_/550437", "title"=>"Overview of the genome data obtained.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-12 00:07:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/879898"], "description"=>"<p>All traditional DNA fingerprints for both isolates were isogenic, with the exception of the MIRU-VNTR locus 1955. K-2 was resistant to all five first line antibiotics (S (sensitive), R (resistant)).</p>", "links"=>[], "tags"=>["strains"], "article_id"=>550337, "categories"=>["Infectious Diseases", "Medicine", "Microbiology", "Genetics", "Virology"], "users"=>["Stefan Niemann", "Claudio U. Köser", "Sebastien Gagneux", "Claudia Plinke", "Susanne Homolka", "Helen Bignell", "Richard J. Carter", "R. Keira Cheetham", "Anthony Cox", "Niall A. Gormley", "Paula Kokko-Gonzales", "Lisa J. Murray", "Roberto Rigatti", "Vincent P. Smith", "Felix P. M. Arends", "Helen S. Cox", "Geoff Smith", "John A. C. Archer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007407.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotyping_and_drug_resistance_data_of_the_strains_analysed_/550337", "title"=>"Genotyping and drug resistance data of the strains analysed.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-12 00:05:37"}

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  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
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Relative Metric

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