BACKGROUND A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret whole-genome sequencing data for genotypic drug susceptibility testing (DST). METHODS We investigated mutations in 92 genes implicated in resistance to 21 anti-tuberculosis drugs using the genomes of 405 phylogenetically diverse MTBC strains. The role of phylogenetically informative mutations was assessed by routine phenotypic DST data for the first-line drugs isoniazid, rifampicin, ethambutol, and pyrazinamide from a separate collection of over 7000 clinical strains. Selected mutations/strains were further investigated by minimum inhibitory concentration (MIC) testing. RESULTS Out of 547 phylogenetically informative mutations identified, 138 were classified as not correlating with resistance to first-line drugs. MIC testing did not reveal a discernible impact of a Rv1979c deletion shared by M. africanum lineage 5 strains on resistance to clofazimine. Finally, we found molecular evidence that some MTBC subgroups may be hyper-susceptible to bedaquiline and clofazimine by different loss-of-function mutations affecting a drug efflux pump subunit (MmpL5). CONCLUSIONS Our findings underline that the genetic diversity in MTBC has to be studied more systematically to inform the design of clinical trials and to define sound epidemiologic cut-off values (ECOFFs) for new and repurposed anti-tuberculosis drugs. In that regard, our comprehensive variant catalogue provides a solid basis for the interpretation of mutations in genotypic as well as in phenotypic DST assays.

中文翻译：

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结核分枝杆菌复合体抗生素耐药性相关基因的系统发育信息突变。


背景需要全面了解结核分枝杆菌复合体（MTBC）中与抗生素耐药性相关的基因中预先存在的遗传变异，以准确解释基因型药物敏感性测试（DST）的全基因组测序数据。方法 我们使用 405 个系统发育不同的 MTBC 菌株的基因组研究了与 21 种抗结核药物耐药性有关的 92 个基因的突变。通过一线药物异烟肼、利福平、乙胺丁醇和吡嗪酰胺的常规表型 DST 数据评估系统发育信息突变的作用，这些数据来自 7000 多个临床菌株的单独收集。通过最低抑菌浓度 (MIC) 测试进一步研究选定的突变/菌株。结果 在确定的 547 个系统发育信息突变中，有 138 个被归类为与一线药物耐药性无关。 MIC 测试并未揭示非洲分枝杆菌谱系 5 菌株共有的 Rv1979c 缺失对氯法齐明耐药性的明显影响。最后，我们发现分子证据表明，一些 MTBC 亚群可能因影响药物外排泵亚基 (MmpL5) 的不同功能丧失突变而对贝达喹啉和氯法齐明高度敏感。结论 我们的研究结果强调，必须更系统地研究 MTBC 的遗传多样性，以便为临床试验的设计提供信息，并为新的和重新利用的抗结核药物定义合理的流行病学临界值 (ECOFF)。在这方面，我们全面的变异目录为解释基因型和表型 DST 检测中的突变提供了坚实的基础。