结核分枝杆菌利福平耐药菌株补偿性突变的系统性鉴定

Comprehensive identification of compensatory mutations in rifampicin-resistant Mycobacterium tuberculosis strains

目的系统性鉴定MTB利福平耐药菌株rpoA、rpoB及rpoC基因补偿性突变的类型，评估不同rpoB基因耐药突变类型及MTB遗传背景对补偿性突变发生的影响。方法搜索并下载已发表的MTB全基因组测序数据，根据已知的利福平耐药突变从中鉴定出利福平耐药的MTB株，构建系统发育树并利用平行进化的筛选标准鉴定出可能的补偿性突变；统计不同rpoB基因耐药突变类型和不同型的利福平耐药菌株携带补偿性突变的比例，利用卡方检验进行统计学分析。结果从欧洲核酸序列数据库共获得全球8 453株MTB全基因组测序数据（覆盖12个国家），其中1 749株为利福平耐药菌株。通过系统发育分析共鉴定出60种补偿性突变类型（rpoA基因上的突变6种，rpoB基因上的突变16种，rpoC基因上的突变38种）；携带rpoB S450L突变的利福平耐药菌株（41.7%，279/669）比其他利福平耐药突变积累补偿性突变的比例更高[8.0%（31/388），χ2＝378.5，P〈0.000 1]；2型的利福平耐药菌株（34.0%）比其他型的菌株积累补偿性突变的比例更高[1型：4.7%（2/43），3型：12.5%（4/32），4型：15.1%（78/517）；χ2＝238.5，P〈0.000 1]。结论本研究系统性鉴定了MTB利福平耐药相关的补偿性突变类型，并发现携带rpoB基因S450L突变或属于2型的利福平耐药菌株更容易积累补偿性突变。

ObjectiveTo comprehensively identify compensatory mutations in rpoA, rpoB and rpoC genes of rifampicin-resistant Mycobacterium tuberculosis （RIF-r MTB） and to evaluate the effect of rifampicin-resistant mutation type and lineage background on occurrence of compensatory mutations.MethodsPublished MTB whole genome sequencing data were searched and downloaded. RIF-r MTB was identified through known rifampicin-resistant mutations. Based on parallel evolutionary patterns, we identified putative compensatory mutations in the phylogenetic tree and calculated proportions of accumulating compensatory mutations in each rifampicin-resistant mutations′ type and lineage background of RIF-r MTB. Statistic significance was analyzed by chi-square test.ResultsA total of 8 453 global MTB whole genome sequencing data were downloaded form ENA （covering 12 countries）, including 1 749 RIF-r MTB. Based on phylogenetic analysis, we totally identified 60 putative compensatory mutations （6 in rpoA gene, 16 in rpoB gene and 38 in rpoC gene）, 11 of which were newly reported. RIF-R strains carrying rpoB S450L （41.7%, 279/669） had a significant higher chance to accumulate compensatory mutations than strains with other rpoB mutations （8.0%, 31/388, χ2=378.5, P〈0.000 1）. In addition, RIF-R strains from lineage 2 （34.0%, 223/656） had a significant higher chance to accumulate compensatory mutations than strains from other lineages [lineage1： 4.7%（2/43）, 2/43, lineage3： 12.5%（4/32）, 4/32, lineage4： 15.1%（78/517）, 78/517; χ2=238.5, P〈0.000 1].ConclusionsOur study comprehensively identified putative rifampicin-resistant compensatory mutations of rifampicin resistance. RIF-R strains carrying rpoB S450L mutation or from lineage 2 had a significantly higher chance to accumulate compensatory mutations than strains either with other rpoB mutations or from other lineages.