Abstract
BackgroundMycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the genome over relevant timescales is required.MethodsWe attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years.ResultsMultiple analyses support an average mutation rate of ~0.3 SNPs per genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links.ConclusionsThis in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole genome sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing.
Highlights
Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing attractive for clinical and epidemiological investigation
For example Gardy et al found that variable number of tandem repeats (VNTR) typing data suggested a tuberculosis outbreak in Canada was clonal, whereas whole genome sequencing data revealed that there were two concurrent outbreaks [6]
In summary, the low mutation rate of M. tuberculosis means that even at the highest resolution provided by whole genome sequencing it is still difficult to confidently affirm the inferences of transmission made by traditional epidemiological techniques
Summary
Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing attractive for clinical and epidemiological investigation. RFLP and VNTR typing may suffer from a slow genetic turn over that reduces their usefulness when epidemiological clusters grow over extended time periods. In such case the distinction between spread from primary, secondary, tertiary, etc., sources in the cluster becomes impossible. Whole genome sequencing allows investigation into genomic evolution and transmission at the highest resolution This level of information can help refine conclusions drawn from traditional fingerprinting methods. The application of sequencing to a large outbreak in Harlingen, the Netherlands, provided a higher resolution picture than could be inferred from typing alone, and reduced the possible number of infection routes for all patients, which agreed with epidemiological investigations [7]
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