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Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

Llinos Harris Orcid Logo, Rhys Jones, Marcela Sandoval Velasco, Llinos G. Harris, Sue Morgan, Mark Temple, Michael C Ruddy, Rhian Williams, Michael D Perry, Matt Hitchings, Thomas Wilkinson Orcid Logo, Thomas Humphrey, M. Thomas P. Gilbert, Angharad Davies Orcid Logo

Tuberculosis, Volume: 119, Start page: 101865

Swansea University Authors: Llinos Harris Orcid Logo, Thomas Wilkinson Orcid Logo, Angharad Davies Orcid Logo

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Abstract

This study describes the analysis of DNA from heat-killed (boilate) isolates of Mycobacterium tuberculosis from two UK outbreaks where DNA was of sub-optimal quality for the standard methodologies routinely used in microbial genomics. An Illumina library construction method developed for sequencing...

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Published in: Tuberculosis
ISSN: 14729792
Published: 2019
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URI: https://cronfa.swan.ac.uk/Record/cronfa51995
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spelling 2019-10-18T15:55:12.3007381 v2 51995 2019-09-23 Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies dc70f9d4badbbdb5d467fd321986d173 0000-0002-0295-3038 Llinos Harris Llinos Harris true false 86cca6bf31bfe8572de27c1b441420d8 0000-0003-0397-6079 Thomas Wilkinson Thomas Wilkinson true false 62586459693e05b2e1063967e76883f1 0000-0003-4190-8894 Angharad Davies Angharad Davies true false 2019-09-23 BMS This study describes the analysis of DNA from heat-killed (boilate) isolates of Mycobacterium tuberculosis from two UK outbreaks where DNA was of sub-optimal quality for the standard methodologies routinely used in microbial genomics. An Illumina library construction method developed for sequencing ancient DNA was successfully used to obtain whole genome sequences, allowing analysis of the outbreak by gene-by-gene MLST, SNP mapping and phylogenetic analysis. All cases were spoligotyped to the same Haarlem H1 sub-lineage. This is the first described application of ancient DNA library construction protocols to allow whole genome sequencing of a clinical tuberculosis outbreak. Using this method it is possible to obtain epidemiologically meaningful data even when DNA is of insufficient quality for standard methods. Journal Article Tuberculosis 119 101865 14729792 Mycobacterium tuberculosis, whole genome sequencing, outbreak investigation, ancient DNA library construction, palaeogenomics 30 9 2019 2019-09-30 10.1016/j.tube.2019.101865 COLLEGE NANME Biomedical Sciences COLLEGE CODE BMS Swansea University 2019-10-18T15:55:12.3007381 2019-09-23T10:09:26.1476866 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Llinos Harris 0000-0002-0295-3038 1 Rhys Jones 2 Marcela Sandoval Velasco 3 Llinos G. Harris 4 Sue Morgan 5 Mark Temple 6 Michael C Ruddy 7 Rhian Williams 8 Michael D Perry 9 Matt Hitchings 10 Thomas Wilkinson 0000-0003-0397-6079 11 Thomas Humphrey 12 M. Thomas P. Gilbert 13 Angharad Davies 0000-0003-4190-8894 14 0051995-01102019155235.pdf 51995.pdf 2019-10-01T15:52:35.2500000 Output 509183 application/pdf Accepted Manuscript true 2020-09-23T00:00:00.0000000 Released under the terms of a Creative Commons Attribution Non-Commercial No Derivatives License (CC-BY-NC-ND). true eng
title Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies
spellingShingle Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies
Llinos Harris
Thomas Wilkinson
Angharad Davies
title_short Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies
title_full Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies
title_fullStr Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies
title_full_unstemmed Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies
title_sort Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies
author_id_str_mv dc70f9d4badbbdb5d467fd321986d173
86cca6bf31bfe8572de27c1b441420d8
62586459693e05b2e1063967e76883f1
author_id_fullname_str_mv dc70f9d4badbbdb5d467fd321986d173_***_Llinos Harris
86cca6bf31bfe8572de27c1b441420d8_***_Thomas Wilkinson
62586459693e05b2e1063967e76883f1_***_Angharad Davies
author Llinos Harris
Thomas Wilkinson
Angharad Davies
author2 Llinos Harris
Rhys Jones
Marcela Sandoval Velasco
Llinos G. Harris
Sue Morgan
Mark Temple
Michael C Ruddy
Rhian Williams
Michael D Perry
Matt Hitchings
Thomas Wilkinson
Thomas Humphrey
M. Thomas P. Gilbert
Angharad Davies
format Journal article
container_title Tuberculosis
container_volume 119
container_start_page 101865
publishDate 2019
institution Swansea University
issn 14729792
doi_str_mv 10.1016/j.tube.2019.101865
college_str Faculty of Medicine, Health and Life Sciences
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hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
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description This study describes the analysis of DNA from heat-killed (boilate) isolates of Mycobacterium tuberculosis from two UK outbreaks where DNA was of sub-optimal quality for the standard methodologies routinely used in microbial genomics. An Illumina library construction method developed for sequencing ancient DNA was successfully used to obtain whole genome sequences, allowing analysis of the outbreak by gene-by-gene MLST, SNP mapping and phylogenetic analysis. All cases were spoligotyped to the same Haarlem H1 sub-lineage. This is the first described application of ancient DNA library construction protocols to allow whole genome sequencing of a clinical tuberculosis outbreak. Using this method it is possible to obtain epidemiologically meaningful data even when DNA is of insufficient quality for standard methods.
published_date 2019-09-30T04:00:26Z
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