Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

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

doi:10.1016/j.tube.2019.101865

Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

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

^*Corresponding author for this work

Section for Hologenomics

Research output: Contribution to journal › Journal article › Research › peer-review

1 Citation (Scopus)

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 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.

Original language	English
Article number	101865
Journal	Tuberculosis
Volume	119
Number of pages	5
ISSN	1472-9792
DOIs	https://doi.org/10.1016/j.tube.2019.101865
Publication status	Published - Dec 2019

Keywords

Ancient DNA library construction
Mycobacterium tuberculosis
Outbreak investigation
Palaeogenomics
Whole genome sequencing

Access to Document

10.1016/j.tube.2019.101865

Cite this

Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies. / Jones, Rhys; Velasco, Marcela Sandoval; Harris, Llinos G.; Morgan, Sue; Temple, Mark; Ruddy, Michael C.; Williams, Rhian; Perry, Michael D.; Hitchings, Matt; Wilkinson, Thomas S.; Humphrey, Thomas; Gilbert, M. Thomas P.; Davies, Angharad P.

In: Tuberculosis, Vol. 119, 101865, 12.2019.

Research output: Contribution to journal › Journal article › Research › peer-review

Jones, Rhys ; Velasco, Marcela Sandoval ; Harris, Llinos G. ; Morgan, Sue ; Temple, Mark ; Ruddy, Michael C. ; Williams, Rhian ; Perry, Michael D. ; Hitchings, Matt ; Wilkinson, Thomas S. ; Humphrey, Thomas ; Gilbert, M. Thomas P. ; Davies, Angharad P. / Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies. In: Tuberculosis. 2019 ; Vol. 119.

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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 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.",

keywords = "Ancient DNA library construction, Mycobacterium tuberculosis, Outbreak investigation, Palaeogenomics, Whole genome sequencing",

author = "Rhys Jones and Velasco, {Marcela Sandoval} and Harris, {Llinos G.} and Sue Morgan and Mark Temple and Ruddy, {Michael C.} and Rhian Williams and Perry, {Michael D.} and Matt Hitchings and Wilkinson, {Thomas S.} and Thomas Humphrey and Gilbert, {M. Thomas P.} and Davies, {Angharad P.}",

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AU - Velasco, Marcela Sandoval

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AU - Temple, Mark

AU - Ruddy, Michael C.

AU - Williams, Rhian

AU - Perry, Michael D.

AU - Hitchings, Matt

AU - Wilkinson, Thomas S.

AU - Humphrey, Thomas

AU - Gilbert, M. Thomas P.

AU - Davies, Angharad P.

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AB - 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.

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KW - Outbreak investigation

KW - Palaeogenomics

KW - Whole genome sequencing

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