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Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing
Tuberculosis disproportionately affects the Canadian Inuit. To address this, it is imperative we understand transmission dynamics in this population. We investigate whether ‘deep’ sequencing can provide additional resolution compared to standard sequencing, using a well-characterized outbreak from t...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012596/ https://www.ncbi.nlm.nih.gov/pubmed/32014110 http://dx.doi.org/10.7554/eLife.53245 |
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author | Lee, Robyn S Proulx, Jean-François McIntosh, Fiona Behr, Marcel A Hanage, William P |
author_facet | Lee, Robyn S Proulx, Jean-François McIntosh, Fiona Behr, Marcel A Hanage, William P |
author_sort | Lee, Robyn S |
collection | PubMed |
description | Tuberculosis disproportionately affects the Canadian Inuit. To address this, it is imperative we understand transmission dynamics in this population. We investigate whether ‘deep’ sequencing can provide additional resolution compared to standard sequencing, using a well-characterized outbreak from the Arctic (2011–2012, 50 cases). Samples were sequenced to ~500–1000x and reads were aligned to a novel local reference genome generated with PacBio SMRT sequencing. Consensus and heterogeneous variants were identified and compared across genomes. In contrast with previous genomic analyses using ~50x depth, deep sequencing allowed us to identify a novel super-spreader who likely transmitted to up to 17 other cases during the outbreak (35% of the remaining cases that year). It is increasingly evident that within-host diversity should be incorporated into transmission analyses; deep sequencing may facilitate more accurate detection of super-spreaders and transmission clusters. This has implications not only for TB, but all genomic studies of transmission - regardless of pathogen. |
format | Online Article Text |
id | pubmed-7012596 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-70125962020-02-12 Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing Lee, Robyn S Proulx, Jean-François McIntosh, Fiona Behr, Marcel A Hanage, William P eLife Epidemiology and Global Health Tuberculosis disproportionately affects the Canadian Inuit. To address this, it is imperative we understand transmission dynamics in this population. We investigate whether ‘deep’ sequencing can provide additional resolution compared to standard sequencing, using a well-characterized outbreak from the Arctic (2011–2012, 50 cases). Samples were sequenced to ~500–1000x and reads were aligned to a novel local reference genome generated with PacBio SMRT sequencing. Consensus and heterogeneous variants were identified and compared across genomes. In contrast with previous genomic analyses using ~50x depth, deep sequencing allowed us to identify a novel super-spreader who likely transmitted to up to 17 other cases during the outbreak (35% of the remaining cases that year). It is increasingly evident that within-host diversity should be incorporated into transmission analyses; deep sequencing may facilitate more accurate detection of super-spreaders and transmission clusters. This has implications not only for TB, but all genomic studies of transmission - regardless of pathogen. eLife Sciences Publications, Ltd 2020-02-04 /pmc/articles/PMC7012596/ /pubmed/32014110 http://dx.doi.org/10.7554/eLife.53245 Text en © 2020, Lee et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Epidemiology and Global Health Lee, Robyn S Proulx, Jean-François McIntosh, Fiona Behr, Marcel A Hanage, William P Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing |
title | Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing |
title_full | Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing |
title_fullStr | Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing |
title_full_unstemmed | Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing |
title_short | Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing |
title_sort | previously undetected super-spreading of mycobacterium tuberculosis revealed by deep sequencing |
topic | Epidemiology and Global Health |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012596/ https://www.ncbi.nlm.nih.gov/pubmed/32014110 http://dx.doi.org/10.7554/eLife.53245 |
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