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Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data

Llinos Harris Orcid Logo, R.C. Jones, L.G. Harris, S. Morgan, M.C. Ruddy, M. Perry, R. Williams, T. Humphrey, M. Temple, A.P. Davies, Angharad Davies Orcid Logo

Journal of Clinical Microbiology

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

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DOI (Published version): 10.1128/JCM.02025-18

Abstract

Inability to standardize the bioinformatic data produced by whole genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, using Ridom Seqsphere software for core genome ML...

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Published in: Journal of Clinical Microbiology
ISSN: 0095-1137 1098-660X
Published: 2019
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URI: https://cronfa.swan.ac.uk/Record/cronfa50080
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spelling 2019-09-17T15:00:17.3392220 v2 50080 2019-04-24 Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data dc70f9d4badbbdb5d467fd321986d173 0000-0002-0295-3038 Llinos Harris Llinos Harris true false 62586459693e05b2e1063967e76883f1 0000-0003-4190-8894 Angharad Davies Angharad Davies true false 2019-04-24 BMS Inability to standardize the bioinformatic data produced by whole genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, using Ridom Seqsphere software for core genome MLST (cgMLST) analysis of whole genome sequencing data. The phylogenetics of tuberculosis in Wales has not previously been studied. Sixty-six Mycobacterium tuberculosis isolates (including 42 outbreak-associated isolates) from South Wales were sequenced using an Illumina platform. Isolates were assigned to Principal Genetic Groups, Single Nucleotide Polymorphism (SNP) cluster groups, lineages and sub-lineages using SNP-calling protocols. WGS data were submitted to the Ridom SeqSphere software for cgMLST analysis and analysed alongside 179 previously lineage-defined isolates. The dataset was dominated by the Euro-American lineage, with the sub-lineage composition being dominated by T, X and Haarlem family strains. The cgMLST analysis successfully assigned 58 isolates to major lineages and results were consistent with those obtained by traditional SNP mapping methods. In addition, the cgMLST scheme was used to resolve an outbreak of tuberculosis occurring in the region. This study supports the use of a cgMLST method for standardized phylogenetic assignment of tuberculosis isolates and for outbreak resolution, and provides the first insight into Welsh tuberculosis phylogenetics, identifying the presence of the Haarlem sub-lineage commonly associated with virulent traits. Journal Article Journal of Clinical Microbiology 0095-1137 1098-660X Mycobacterium tuberculosis; phylogenetics; whole genome sequencing; Wales; UK 31 12 2019 2019-12-31 10.1128/JCM.02025-18 COLLEGE NANME Biomedical Sciences COLLEGE CODE BMS Swansea University 2019-09-17T15:00:17.3392220 2019-04-24T14:43:38.3007807 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Llinos Harris 0000-0002-0295-3038 1 R.C. Jones 2 L.G. Harris 3 S. Morgan 4 M.C. Ruddy 5 M. Perry 6 R. Williams 7 T. Humphrey 8 M. Temple 9 A.P. Davies 10 Angharad Davies 0000-0003-4190-8894 11 0050080-15052019115013.pdf 50080.pdf 2019-05-15T11:50:13.1300000 Output 224040 application/pdf Accepted Manuscript true 2019-10-03T00:00:00.0000000 true eng
title Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data
spellingShingle Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data
Llinos Harris
Angharad Davies
title_short Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data
title_full Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data
title_fullStr Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data
title_full_unstemmed Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data
title_sort Phylogenetic analysis of Mycobacterium tuberculosis strains in Wales using core genome MLST to analyse whole genome sequencing data
author_id_str_mv dc70f9d4badbbdb5d467fd321986d173
62586459693e05b2e1063967e76883f1
author_id_fullname_str_mv dc70f9d4badbbdb5d467fd321986d173_***_Llinos Harris
62586459693e05b2e1063967e76883f1_***_Angharad Davies
author Llinos Harris
Angharad Davies
author2 Llinos Harris
R.C. Jones
L.G. Harris
S. Morgan
M.C. Ruddy
M. Perry
R. Williams
T. Humphrey
M. Temple
A.P. Davies
Angharad Davies
format Journal article
container_title Journal of Clinical Microbiology
publishDate 2019
institution Swansea University
issn 0095-1137
1098-660X
doi_str_mv 10.1128/JCM.02025-18
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
document_store_str 1
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description Inability to standardize the bioinformatic data produced by whole genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, using Ridom Seqsphere software for core genome MLST (cgMLST) analysis of whole genome sequencing data. The phylogenetics of tuberculosis in Wales has not previously been studied. Sixty-six Mycobacterium tuberculosis isolates (including 42 outbreak-associated isolates) from South Wales were sequenced using an Illumina platform. Isolates were assigned to Principal Genetic Groups, Single Nucleotide Polymorphism (SNP) cluster groups, lineages and sub-lineages using SNP-calling protocols. WGS data were submitted to the Ridom SeqSphere software for cgMLST analysis and analysed alongside 179 previously lineage-defined isolates. The dataset was dominated by the Euro-American lineage, with the sub-lineage composition being dominated by T, X and Haarlem family strains. The cgMLST analysis successfully assigned 58 isolates to major lineages and results were consistent with those obtained by traditional SNP mapping methods. In addition, the cgMLST scheme was used to resolve an outbreak of tuberculosis occurring in the region. This study supports the use of a cgMLST method for standardized phylogenetic assignment of tuberculosis isolates and for outbreak resolution, and provides the first insight into Welsh tuberculosis phylogenetics, identifying the presence of the Haarlem sub-lineage commonly associated with virulent traits.
published_date 2019-12-31T04:01:23Z
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