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Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies.

Rhys Jones1, Marcela Sandoval Velasco2, Llinos G Harris1

  • 1Swansea University Medical School, Institute of Life Science, Swansea University, Swansea, Wales, UK.

Tuberculosis (Edinburgh, Scotland)
|September 30, 2019
PubMed
Summary
This summary is machine-generated.

Researchers successfully sequenced low-quality DNA from Mycobacterium tuberculosis outbreaks using ancient DNA methods. This approach enables robust genomic analysis for tracking infectious disease, even with challenging samples.

Keywords:
Ancient DNA library constructionMycobacterium tuberculosisOutbreak investigationPalaeogenomicsWhole genome sequencing

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Area of Science:

  • Genomics
  • Microbiology
  • Epidemiology

Background:

  • Standard microbial genomics methods struggle with sub-optimal DNA quality.
  • Mycobacterium tuberculosis outbreaks pose challenges for traditional genetic analysis.

Purpose of the Study:

  • To adapt ancient DNA (aDNA) library construction for sequencing clinical Mycobacterium tuberculosis outbreak isolates.
  • To evaluate the utility of aDNA methods for whole genome sequencing (WGS) of compromised DNA samples.

Main Methods:

  • Utilized an Illumina library construction protocol designed for ancient DNA.
  • Applied gene-by-gene Multi-Locus Sequence Typing (MLST), Single Nucleotide Polymorphism (SNP) mapping, and phylogenetic analysis.
  • Spoligotyped all isolates to the Haarlem H1 sub-lineage.

Main Results:

  • Successfully obtained whole genome sequences from heat-killed Mycobacterium tuberculosis isolates with sub-optimal DNA quality.
  • Demonstrated the feasibility of WGS using aDNA protocols for clinical outbreak samples.
  • Confirmed all cases belonged to the Haarlem H1 sub-lineage, enabling outbreak analysis.

Conclusions:

  • Ancient DNA library construction protocols are effective for whole genome sequencing of clinical tuberculosis outbreaks.
  • This methodology allows for epidemiologically meaningful data acquisition from compromised DNA.
  • The study presents the first application of aDNA protocols for clinical tuberculosis outbreak WGS.