The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.

中文翻译：

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基于7547个基因组图谱，对175个非结核分枝杆菌物种进行了全面的亚种鉴定。

在世界范围内，非结核分枝杆菌（NTM）肺部疾病的患病率正在上升。NTM由大约200种组成，在亚种水平上区分它们对于治疗至关重要。在这项研究中，我们使用来自Illumina和Oxford Nanopore Technologies（ONT）的测序仪通过杂交装配对63个NTM基因组进行了测序，其中27个是新确定的。该分析将可用的基因组数据扩展到175个NTM物种，并重新定义了其亚属分类。我们还基于7547个装配体中的184个基因开发了一种新颖的多基因座序列分类（MLST）数据库，并使用mlstverse鉴定软件，只要合适的MLST数据库，该软件也可用于检测其他细菌。该方法在常规方法中显示出最高的灵敏度和特异性，并展示了快速检测NTM的能力，ONT MinION测序10分钟就足够了。该方法的应用可以改善疾病流行病学并提高NTM疾病的治愈率。