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dc.contributor.authorBlack, PA
dc.contributor.authorde Vos, M.
dc.contributor.authorLouw, GE
dc.contributor.authorvan der Merwe, RG
dc.contributor.authorDippenaar, A.
dc.contributor.authorStreicher, EM
dc.contributor.authorAbdallah, A. M.
dc.contributor.authorSampson, SL
dc.contributor.authorVictor, TC
dc.contributor.authorDolby, T.
dc.contributor.authorSimpson, JA
dc.contributor.authorvan Helden, PD
dc.contributor.authorWarren, RM
dc.contributor.authorPain, Arnab
dc.date.accessioned2015-11-05T06:58:36Z
dc.date.available2015-11-05T06:58:36Z
dc.date.issued2015-10-24
dc.identifier.citationWhole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates 2015, 16 (1) BMC Genomics
dc.identifier.issn1471-2164
dc.identifier.pmid26496891
dc.identifier.doi10.1186/s12864-015-2067-2
dc.identifier.urihttp://hdl.handle.net/10754/581783
dc.description.abstractBackground Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis. Methods Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline. Results Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30 % to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event. Conclusions Our study demonstrated true levels of genetic diversity within an M. tuberculosis population and showed that genetic diversity may be re-defined when a selective pressure, such as drug exposure, is imposed on M. tuberculosis populations during the course of infection. This suggests that the genome of M. tuberculosis is more dynamic than previously thought, suggesting preparedness to respond to a changing environment.
dc.language.isoen
dc.publisherSpringer Nature
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/16/857
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.subjectGenetic complexity
dc.subjectClinical isolates
dc.subjectMycobacterium tuberculosis
dc.subjectHeterogeneity
dc.subjectNext generation sequencing
dc.subjectRelaxed variant filtering
dc.titleWhole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalBMC Genomics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
dc.contributor.institutionNational Health Laboratory Services, Green Point, Cape Town, South Africa
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personPain, Arnab
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.c.3596495
refterms.dateFOA2018-06-14T03:08:34Z
display.relations<b> Is Supplemented By:</b> <br/> <ul><li><i>[Dataset]</i> <br/> PA Black, M. De Vos, GE Louw, RG Van Der Merwe, A. Dippenaar, EM Streicher, … A. Pain. (2015). Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates. Figshare. https://doi.org/10.6084/m9.figshare.c.3596495. DOI: <a href="https://doi.org/10.6084/m9.figshare.c.3596495">10.6084/m9.figshare.c.3596495</a> HANDLE: <a href="http://hdl.handle.net/10754/624126">10754/624126</a></li></ul>
dc.date.published-online2015-10-24
dc.date.published-print2015-12


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