基于全基因组测序估算结核分枝杆菌分子钟

Estimation of molecular clock of Mycobacterium tuberculosis based on whole genome sequencing data

目的基于全基因组测序数据,通过内源性激活期间菌株基因组突变分析,开展结核分枝杆菌(MTB)分子钟研究。方法筛选MTB内源性激活全基因组研究文献,下载全基因组测序数据,提取初治-复发配对样本单核苷酸多态性(SNP)差异和菌株分离时间,运用Poisson回归模型拟合初治-复发时间间隔与差异SNP的关系,计算MTB分子钟,估算突变率。结果若MTB传代时间为18 h,0~2年短期内源性激活突变率为6.47×10^(-10)(95%CI:5.59×10^(-10)~7.44×10^(-10)),明显高于2~14年长期内源性激活突变率(3.27×10^(-10),95%CI:2.88×10^(-10)~3.69×10^(-10))。0~、1~、2~、3~、5~、7~14年突变率分别为7.10×10^(-10)、6.06×10^(-10)、4.24×10^(-10)、5.34×10^(-10)、2.59×10^(-10)、1.26×10^(-10)。结论内源性激活复发期间,MTB突变率随初治-复发时间间隔增加而下降,本研究从微观层面验证了临床实践观察到的初治结核病2年内易复发现象。

Objective To analyze the genomic mutation of Mycobacterium tuberculosis(M.tuberculosis)isolated in endogenous activation period and estimate the molecular clock based on the whole genome sequencing data.Methods Literatures of the whole genome research of endogenous reactivated tuberculosis were retrieved,and the corresponding whole genome sequencing data were downloaded.We extracted the single nucleotide polymorphisms(SNPs)and strain isolation time of initial treatment and relapse of tuberculosis cases,explored the relationship between the different SNPs and interval between initial treatment and relapse by Poisson regression model,calculated the M.tuberculosis molecular clock,and estimated the mutation rate.Results When the generation time of M.tuberculosis was 18 hours,the mutation rate in 0-2 years,i.e.short-term endogenous activation,was 6.47×10^(-10)(95%CI:5.59×10^(-10)-7.44×10^(-10)),which was significantly higher than that in 2-14 years in long term endogenous activation(3.27×10^(-10),95%CI 2.88×10^(-10)-3.69×10^(-10)).The mutation rates of 0-,1-,2-,3-,5-and 7-14 years were 7.10×10^(-10),6.06×10^(-10),4.24×10^(-10),5.34×10^(-10),2.59×10^(-10) and 1.26×10^(-10) respectively.Conclusions In the period of endogenous reactivation,the mutation rate of M.tuberculosis decreases with the interval time between initial treatment and relapse,which verifies the clinically observed phenomenon that the relapse often occurs within two years after the initial treatment of tuberculosis.