Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

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

doi:10.1016/j.tube.2019.101865

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Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

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

Tuberculosis, Volume: 119, Start page: 101865

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

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DOI (Published version): 10.1016/j.tube.2019.101865

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
Online Access:	Check full text
URI:	https://cronfa.swan.ac.uk/Record/cronfa51995
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first_indexed	2019-09-23T14:18:29Z
last_indexed	2019-10-18T20:22:20Z
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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
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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	2019-09-30T04:04:06Z
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Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

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