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

Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, Flynn JL, Fortune SM - Nat. Genet. (2011)

Bottom Line: Based on the distribution of SNPs observed, we calculated the mutation rates for these disease states.The pattern of polymorphisms suggests that the mutational burden in vivo is because of oxidative DNA damage.We show that Mtb continues to acquire mutations during disease latency, which may explain why isoniazid monotherapy for latent tuberculosis is a risk factor for the emergence of isoniazid resistance.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA.

ABSTRACT
Tuberculosis poses a global health emergency, which has been compounded by the emergence of drug-resistant Mycobacterium tuberculosis (Mtb) strains. We used whole-genome sequencing to compare the accumulation of mutations in Mtb isolated from cynomolgus macaques with active, latent or reactivated disease. We sequenced 33 Mtb isolates from nine macaques with an average genome coverage of 93% and an average read depth of 117×. Based on the distribution of SNPs observed, we calculated the mutation rates for these disease states. We found a similar mutation rate during latency as during active disease or in a logarithmically growing culture over the same period of time. The pattern of polymorphisms suggests that the mutational burden in vivo is because of oxidative DNA damage. We show that Mtb continues to acquire mutations during disease latency, which may explain why isoniazid monotherapy for latent tuberculosis is a risk factor for the emergence of isoniazid resistance.

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Mutations in Mtb isolated from macaques with latent infection and related human isolates are putative products of oxidative damage(a) Ten of the fourteen mutations observed in this study could be the product of oxidative damage: the deamination of cytosine (GC>AT) or the production of 7,8-dihydro-8-oxoguanine (GC>TA) by the oxidation of guanine. One of each type of mutation observed was seen in active disease (four mutations total). In contrast, eight of ten mutations observed in latent and reactivated disease are potential products of oxidative damage. There is a similar mutational spectra observed in the synonymous SNPs identified by WGS of a set of closely related strains from South Africa9. (b) These observations lead to a model of mutational pressures on Mtb during active disease and latent infection in which oxidative damage may play a central role in the generation of mutation.
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Figure 4: Mutations in Mtb isolated from macaques with latent infection and related human isolates are putative products of oxidative damage(a) Ten of the fourteen mutations observed in this study could be the product of oxidative damage: the deamination of cytosine (GC>AT) or the production of 7,8-dihydro-8-oxoguanine (GC>TA) by the oxidation of guanine. One of each type of mutation observed was seen in active disease (four mutations total). In contrast, eight of ten mutations observed in latent and reactivated disease are potential products of oxidative damage. There is a similar mutational spectra observed in the synonymous SNPs identified by WGS of a set of closely related strains from South Africa9. (b) These observations lead to a model of mutational pressures on Mtb during active disease and latent infection in which oxidative damage may play a central role in the generation of mutation.

Mentions: An alternative interpretation is that the mutational capacity of Mtb during latent infection is determined primarily by the length of time the organism spends in the host environment rather than the replicative capacity and replicative error of the organism during infection. We noted that eight of the ten polymorphisms that we identified in our isolates from animals with persistent latent or reactivated latent infection are possible products of oxidative damage, either cytosine deamination (GC>AT) or the formation of 8-oxoguanine (GC>TA) (Fig. 4a). This is consistent with the model that Mtb faces an oxidative environment in the macrophage phagolysosome21,22 and data indicating that genes involved in the repair of oxidative damage are essential for bacterial survival during murine infection23. In addition, we found that the pattern of polymorphisms in Mtb from cynomolgus macaques is similar to the pattern of neutral polymorphisms that emerged during the evolution of extensively drug resistant Mtb strains in patients from South Africa (Fig. 4a)9. Thus, the mutational capacity of Mtb during latent infection as well as the spectrum of those mutations suggests that the dominant source of mutation during latency is oxidative DNA damage rather than replicative error24 (Fig. 4b). This may occur because the immune response that results in latent infection causes more oxidative damage to the bacterial DNA14,25 or because a portion of the bacteria may enter a metabolically quiescent state in which DNA repair is diminished26,27.


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

Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, Flynn JL, Fortune SM - Nat. Genet. (2011)

Mutations in Mtb isolated from macaques with latent infection and related human isolates are putative products of oxidative damage(a) Ten of the fourteen mutations observed in this study could be the product of oxidative damage: the deamination of cytosine (GC>AT) or the production of 7,8-dihydro-8-oxoguanine (GC>TA) by the oxidation of guanine. One of each type of mutation observed was seen in active disease (four mutations total). In contrast, eight of ten mutations observed in latent and reactivated disease are potential products of oxidative damage. There is a similar mutational spectra observed in the synonymous SNPs identified by WGS of a set of closely related strains from South Africa9. (b) These observations lead to a model of mutational pressures on Mtb during active disease and latent infection in which oxidative damage may play a central role in the generation of mutation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3101871&req=5

Figure 4: Mutations in Mtb isolated from macaques with latent infection and related human isolates are putative products of oxidative damage(a) Ten of the fourteen mutations observed in this study could be the product of oxidative damage: the deamination of cytosine (GC>AT) or the production of 7,8-dihydro-8-oxoguanine (GC>TA) by the oxidation of guanine. One of each type of mutation observed was seen in active disease (four mutations total). In contrast, eight of ten mutations observed in latent and reactivated disease are potential products of oxidative damage. There is a similar mutational spectra observed in the synonymous SNPs identified by WGS of a set of closely related strains from South Africa9. (b) These observations lead to a model of mutational pressures on Mtb during active disease and latent infection in which oxidative damage may play a central role in the generation of mutation.
Mentions: An alternative interpretation is that the mutational capacity of Mtb during latent infection is determined primarily by the length of time the organism spends in the host environment rather than the replicative capacity and replicative error of the organism during infection. We noted that eight of the ten polymorphisms that we identified in our isolates from animals with persistent latent or reactivated latent infection are possible products of oxidative damage, either cytosine deamination (GC>AT) or the formation of 8-oxoguanine (GC>TA) (Fig. 4a). This is consistent with the model that Mtb faces an oxidative environment in the macrophage phagolysosome21,22 and data indicating that genes involved in the repair of oxidative damage are essential for bacterial survival during murine infection23. In addition, we found that the pattern of polymorphisms in Mtb from cynomolgus macaques is similar to the pattern of neutral polymorphisms that emerged during the evolution of extensively drug resistant Mtb strains in patients from South Africa (Fig. 4a)9. Thus, the mutational capacity of Mtb during latent infection as well as the spectrum of those mutations suggests that the dominant source of mutation during latency is oxidative DNA damage rather than replicative error24 (Fig. 4b). This may occur because the immune response that results in latent infection causes more oxidative damage to the bacterial DNA14,25 or because a portion of the bacteria may enter a metabolically quiescent state in which DNA repair is diminished26,27.

Bottom Line: Based on the distribution of SNPs observed, we calculated the mutation rates for these disease states.The pattern of polymorphisms suggests that the mutational burden in vivo is because of oxidative DNA damage.We show that Mtb continues to acquire mutations during disease latency, which may explain why isoniazid monotherapy for latent tuberculosis is a risk factor for the emergence of isoniazid resistance.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA.

ABSTRACT
Tuberculosis poses a global health emergency, which has been compounded by the emergence of drug-resistant Mycobacterium tuberculosis (Mtb) strains. We used whole-genome sequencing to compare the accumulation of mutations in Mtb isolated from cynomolgus macaques with active, latent or reactivated disease. We sequenced 33 Mtb isolates from nine macaques with an average genome coverage of 93% and an average read depth of 117×. Based on the distribution of SNPs observed, we calculated the mutation rates for these disease states. We found a similar mutation rate during latency as during active disease or in a logarithmically growing culture over the same period of time. The pattern of polymorphisms suggests that the mutational burden in vivo is because of oxidative DNA damage. We show that Mtb continues to acquire mutations during disease latency, which may explain why isoniazid monotherapy for latent tuberculosis is a risk factor for the emergence of isoniazid resistance.

Show MeSH
Related in: MedlinePlus