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...
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ftdoajarticles:oai:doaj.org/article:b296c9effda045c6bc33bb447b5dfc58 2023-05-15T15:04:38+02:00 Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing Robyn S Lee Jean-François Proulx Fiona McIntosh Marcel A Behr William P Hanage 2020-02-01T00:00:00Z https://doi.org/10.7554/eLife.53245 https://doaj.org/article/b296c9effda045c6bc33bb447b5dfc58 EN eng eLife Sciences Publications Ltd https://elifesciences.org/articles/53245 https://doaj.org/toc/2050-084X doi:10.7554/eLife.53245 2050-084X e53245 https://doaj.org/article/b296c9effda045c6bc33bb447b5dfc58 eLife, Vol 9 (2020) Tuberculosis genomic epidemiology within-host diversity transmission outbreaks Medicine R Science Q Biology (General) QH301-705.5 article 2020 ftdoajarticles https://doi.org/10.7554/eLife.53245 2022-12-30T19:48:56Z 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. Article in Journal/Newspaper Arctic inuit Directory of Open Access Journals: DOAJ Articles Arctic eLife 9 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
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Tuberculosis genomic epidemiology within-host diversity transmission outbreaks Medicine R Science Q Biology (General) QH301-705.5 |
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Tuberculosis genomic epidemiology within-host diversity transmission outbreaks Medicine R Science Q Biology (General) QH301-705.5 Robyn S Lee Jean-François Proulx Fiona McIntosh Marcel A Behr William P Hanage Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing |
topic_facet |
Tuberculosis genomic epidemiology within-host diversity transmission outbreaks Medicine R Science Q Biology (General) QH301-705.5 |
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 |
Article in Journal/Newspaper |
author |
Robyn S Lee Jean-François Proulx Fiona McIntosh Marcel A Behr William P Hanage |
author_facet |
Robyn S Lee Jean-François Proulx Fiona McIntosh Marcel A Behr William P Hanage |
author_sort |
Robyn S Lee |
title |
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_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_sort |
previously undetected super-spreading of mycobacterium tuberculosis revealed by deep sequencing |
publisher |
eLife Sciences Publications Ltd |
publishDate |
2020 |
url |
https://doi.org/10.7554/eLife.53245 https://doaj.org/article/b296c9effda045c6bc33bb447b5dfc58 |
geographic |
Arctic |
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Arctic |
genre |
Arctic inuit |
genre_facet |
Arctic inuit |
op_source |
eLife, Vol 9 (2020) |
op_relation |
https://elifesciences.org/articles/53245 https://doaj.org/toc/2050-084X doi:10.7554/eLife.53245 2050-084X e53245 https://doaj.org/article/b296c9effda045c6bc33bb447b5dfc58 |
op_doi |
https://doi.org/10.7554/eLife.53245 |
container_title |
eLife |
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9 |
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1766336370633080832 |