Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies

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. A blunt-end Ligation based DNA library construction method, developed for sequencing ancient degraded DNA, was successfully used to obtain whole genome sequences from the sub-optimal samples. Thus, allowing analysis of the outbreak by WGS gene-by-gene MLST, SNP mapping and phylogenetics to be achieved. 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: Mycobacterium tuberculosis, whole genome sequencing, outbreak investigation, ancient DNA, library construction, palaeogenomics.