Whole Genome Sequencing compared with phenotypic (MGIT) and commercial molecular tests for drug resistant Mycobacterium tuberculosis isolated from patients in Brazil and Mozambique.

This study aimed to use WGS to describe the mutations conferring resistance in clinical isolates of M. tuberculosis from Brazil and Mozambique and to compare these results to those obtained by phenotypic and commercial genotypic DST.Methods: This cross-sectional study evaluated 30 isolates from patients with DR-TB from Brazil and Mozambique. All the isolates were evaluated with phenotypic (MGIT-SIRE) and genotypic (Xpert-MTB/RIF, Genotype-MTBDRplus and MTBDRsl) DST. Any isolate with detected resistance to at least one first- or second-line drug went to WGS, followed by the analysis with TB profiler online tool database. Results: Compared to the phenotypic DST WGS sensitivity and specificity for rifampicin resistance detection was 87.5% and 92.3%; for isoniazid sensitivity was 91.3% and the specificity 100%; for streptomycin sensitivity was 85.7% and specificity 93.3%. Regarding ethambutol sensitivity was 100% and specificity 77.2%. The concordance between WGS and phenotypic DST was 89.6% for rifampicin and streptomycin; 93.1% for isoniazid and 82.7% for ethambutol. In two isolates from Mozambique, there was a mutation in rpoB gene (Val170Phe) which was neither detected by Xpert-MTB/RIF, nor Genotype-MTBDRplus. Conclusion: WGS showed good performance and a great potential to provide more accurate information about the M. tuberculosis resistance in two high-burden areas without previous WGS information.

本研究旨在通过全基因组测序（Whole Genome Sequencing，WGS）描述来自巴西与莫桑比克的临床结核分枝杆菌（Mycobacterium tuberculosis，M. tuberculosis）分离株中与耐药性相关的突变，并将该结果与表型药敏试验（drug susceptibility testing，DST）及商用基因型药敏试验的结果进行对比。
方法：本横断面研究共评估了来自巴西、莫桑比克的耐药结核病（Drug-Resistant TB，DR-TB）患者的30株分离株。所有分离株均接受了表型（MGIT-SIRE）及基因型（Xpert-MTB/RIF、Genotype-MTBDRplus及MTBDRsl）药敏试验检测。对至少对一种一线或二线药物存在耐药性的分离株进行全基因组测序，随后借助TB Profiler在线工具数据库开展分析。
结果：相较于表型药敏试验，全基因组测序检测利福平耐药性的灵敏度为87.5%、特异度为92.3%；检测异烟肼耐药性的灵敏度为91.3%、特异度为100%；检测链霉素耐药性的灵敏度为85.7%、特异度为93.3%。针对乙胺丁醇，其灵敏度为100%、特异度为77.2%。全基因组测序与表型药敏试验的一致性方面，利福平与链霉素为89.6%、异烟肼为93.1%、乙胺丁醇为82.7%。在2株来自莫桑比克的分离株中，发现rpoB基因存在Val170Phe突变，该突变未被Xpert-MTB/RIF及Genotype-MTBDRplus检测到。
结论：全基因组测序展现出良好的检测性能，具备为两个此前无全基因组测序相关数据的高负担地区提供更准确的结核分枝杆菌耐药性信息的巨大潜力。