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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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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 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.
Keywords: Mycobacterium tuberculosis; phylogenetics; whole genome sequencing; Wales; UK
College: Swansea University Medical School