Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

Abstract

Mycobacterium tuberculosis (Mtb) has generated a global health catastrophe that has been compounded by the emergence of drug resistant Mtb strains. We used whole genome sequencing to compare the accumulation of mutations in Mtb isolated from cynomolgus macaques with active, latent and reactivated disease. Based on the distribution of SNPs observed, we calculated the mutation rates for these disease states. Our data suggest that Mtb acquires a similar number of chromosomal mutations during latency as occurs during active disease or in a logarithmically growing culture over the same period of time despite reduced bacterial replication during latent infection. The pattern of polymorphisms suggests that the mutational burden in vivo is due to oxidative DNA damage. Thus, we demonstrate that Mtb continues to acquire mutations during latency and provide a novel explanation for the observation that isoniazid monotherapy for latent tuberculosis is a risk factor for the emergence of INH resistance1,2.

Substantial molecular evolution and mutation rates in prolonged latent Mycobacterium tuberculosis infection in humans

“…Thus, we find an average molecular clock rate of 0.2 -0.3 SNPs per genome per year. Interestingly, this compares quite well to rates of mutation acquisition observed previously in Lineage 4, both in vitro (Ford et al, 2011;Ford et al, 2013) and in several independent retrospective outbreak studies (Eldholm et al, 2015;Guerra-Assuncao et al, 2015;Walker et al, 2013). While current models of Mtb during latency assume that there is little or no growth or mutation of the infecting bacteria, a recent in vitro study using a macaque model has provided evidence that Mtb mutates at a fixed rate over time, and that mutation rates are comparable between latent and active disease (Ford et al, 2011).…”

“…Such processes can be investigated by studying mutational patterns as revealed by genome sequencing. We first examined a previously proposed hypothesis that mutation accumulation during latency is often the product of oxidative damage (Ford et al, 2011). Links 1 and 2 were inspected for molecular signatures indicative of oxidative damage, either cytosine deamination (GC to AT changes) or formation of 8-oxoguanine (GC to TA changes).…”

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

“…tuberculosis phylogeny using the different molecular clocks described in the literature (Bos et al, 2014;Bryant et al, 2013;Comas et al, 2013;Ford et al, 2011;Merker et al, 2015).…”

“…Short-term evolutionary rate in M. tuberculosis complex has been estimated to be between 0.3 and 0.5 punctual mutations per genome per year (also referred to as Single Nucleotide Polymorphism or SNP per genome per year) which corresponds to an annual rate per site of 6.8 x 10 -8 to 1.1 x 10 -7 (Bryant et al, 2013;Ford et al, 2011;Guerra-Assuncao et al, 2015;Roetzer et al, 2013;Walker et al, 2013). Mutation rate was also assessed directly using whole genome sequence of a tuberculosis sample extracted from a 1,000-year old Peruvian mummy: it was measured as 4.8 x 10 -8 SNP/site/year i.e.…”

Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis

“…Mycobacterium tuberculosis is characterized by a low mutation rate (about 2 × 10 −10 mutations/bp/generation) (Ford et al., 2011), with an estimated evolutionary rate of 0.4—0.5 single nucleotide polymorphisms (SNPs)/genome/year and a divergence rarely higher than five SNPs in 3 years (Roetzer et al., 2013; Walker et al., 2013). Despite this low mutation rate, the number of drug resistant, especially MDR and XDR TB cases, due to the acquisition of mutations, is progressively increasing worldwide.…”