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 af dette arbejde

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.

Originalsprog	Engelsk
Artikelnummer	101865
Tidsskrift	Tuberculosis
Vol/bind	119
Antal sider	5
ISSN	1472-9792
DOI	https://doi.org/10.1016/j.tube.2019.101865
Status	Udgivet - dec. 2019

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10.1016/j.tube.2019.101865

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Jones, R., Velasco, M. S., Harris, L. G., Morgan, S., Temple, M., Ruddy, M. C., Williams, R., Perry, M. D., Hitchings, M., Wilkinson, T. S., Humphrey, T., Gilbert, M. T. P., & Davies, A. P. (2019). Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies. Tuberculosis, 119, Artikel 101865. https://doi.org/10.1016/j.tube.2019.101865

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title = "Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies",

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.}",

year = "2019",

month = dec,

doi = "10.1016/j.tube.2019.101865",

language = "English",

volume = "119",

journal = "Tuberculosis",

issn = "1472-9792",

publisher = "Churchill Livingstone",

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TY - JOUR

T1 - Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

AU - Jones, Rhys

AU - Velasco, Marcela Sandoval

AU - Harris, Llinos G.

AU - Morgan, Sue

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.

PY - 2019/12

Y1 - 2019/12

N2 - 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.

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.

KW - Ancient DNA library construction

KW - Mycobacterium tuberculosis

KW - Outbreak investigation

KW - Palaeogenomics

KW - Whole genome sequencing

U2 - 10.1016/j.tube.2019.101865

DO - 10.1016/j.tube.2019.101865

M3 - Journal article

C2 - 31563810

AN - SCOPUS:85072609410

SN - 1472-9792

VL - 119

JO - Tuberculosis

JF - Tuberculosis

M1 - 101865

ER -

Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

Abstract

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