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Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture

BACKGROUND: Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tube...

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Autores principales: Nimmo, Camus, Shaw, Liam P., Doyle, Rona, Williams, Rachel, Brien, Kayleen, Burgess, Carrie, Breuer, Judith, Balloux, Francois, Pym, Alexander S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528373/
https://www.ncbi.nlm.nih.gov/pubmed/31109296
http://dx.doi.org/10.1186/s12864-019-5782-2
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author Nimmo, Camus
Shaw, Liam P.
Doyle, Rona
Williams, Rachel
Brien, Kayleen
Burgess, Carrie
Breuer, Judith
Balloux, Francois
Pym, Alexander S.
author_facet Nimmo, Camus
Shaw, Liam P.
Doyle, Rona
Williams, Rachel
Brien, Kayleen
Burgess, Carrie
Breuer, Judith
Balloux, Francois
Pym, Alexander S.
author_sort Nimmo, Camus
collection PubMed
description BACKGROUND: Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture. RESULTS: DNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p = 0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance. CONCLUSIONS: Culture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5782-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-65283732019-05-28 Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture Nimmo, Camus Shaw, Liam P. Doyle, Rona Williams, Rachel Brien, Kayleen Burgess, Carrie Breuer, Judith Balloux, Francois Pym, Alexander S. BMC Genomics Research Article BACKGROUND: Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture. RESULTS: DNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p = 0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance. CONCLUSIONS: Culture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5782-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-20 /pmc/articles/PMC6528373/ /pubmed/31109296 http://dx.doi.org/10.1186/s12864-019-5782-2 Text en © The Author(s). 2019 Open AccessThis 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.
spellingShingle Research Article
Nimmo, Camus
Shaw, Liam P.
Doyle, Rona
Williams, Rachel
Brien, Kayleen
Burgess, Carrie
Breuer, Judith
Balloux, Francois
Pym, Alexander S.
Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
title Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
title_full Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
title_fullStr Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
title_full_unstemmed Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
title_short Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
title_sort whole genome sequencing mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528373/
https://www.ncbi.nlm.nih.gov/pubmed/31109296
http://dx.doi.org/10.1186/s12864-019-5782-2
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