Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections. Although numerous studies have investigated the genetic variation among prevalent clinical NTM species, including Mycobacterium abscessus and Mycobacterium avium , many of the less common but clinically relevant NTM species, including M. kubicae , still lack complete genomes to serve as a comparative reference. Well-characterized representative genomes for each NTM species are important both for investigating the pathogenic potential of NTM, as well as for use in diagnostic methods, even for species that less frequently cause human disease. Here, we report the complete genomes of two M. kubicae strains, isolated from two unrelated patients. Hybrid short-read and long-read sequencing and assembly, using sequence reads from Illumina and Oxford Nanopore Technologies platforms, were utilized to resolve the chromosome and plasmid sequences of each isolate. The genome of NJH_MKUB1 had 5135 coding sequences (CDSs), a circular chromosome of length 5.3 Mb and two plasmids. The genome of NJH_MKUB2 had 5957 CDSs, a circular chromosome of 6.0 Mb and five plasmids. We compared our completed genomic assemblies to four recently released draft genomes of M. kubicae in order to better understand intraspecies genomic conservation and variability. We also identified genes implicated in drug resistance, virulence and persistence in the M. kubicae chromosome and plasmids. Virulence factors encoded in the genome and in the plasmids of M. kubicae provide a foundation for investigating how opportunistic environmental NTM may cause disease.

中文翻译：

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两种临床分离株全基因组序列揭示库比克分枝杆菌种内质粒和基因组变异

库比克分枝杆菌 是近 200 种非结核分枝杆菌 (NTM) 中的一种，NTM 是一种环境微生物，在某些情况下会感染人类并导致严重的肺、皮肤和软组织感染。尽管许多研究调查了流行的临床 NTM 物种（包括脓肿分枝杆菌和鸟分枝杆菌）之间的遗传变异，但许多不太常见但临床相关的 NTM 物种（包括M.kubicae） ，仍然缺乏完整的基因组作为比较参考。每个 NTM 物种的充分表征的代表性基因组对于研究 NTM 的致病潜力以及在诊断方法中的使用都很重要，甚至对于不太经常引起人类疾病的物种也是如此。在这里，我们报告了两种M. kubicae的完整基因组 菌株，分离自两名无关患者。使用来自 Illumina 和 Oxford Nanopore Technologies 平台的序列读数，使用混合短读长和长读长测序和组装来解析每个分离株的染色体和质粒序列。NJH_MKUB1 基因组有 5135 个编​​码序列 (CDS)、一条长 5.3 Mb 的环状染色体和两个质粒。NJH_MKUB2基因组有5957个CDS，一条6.0 Mb的环状染色体和5个质粒。我们将我们完成的基因组组装与四个最近发布的M. kubicae基因组草图进行了比较，以更好地了解种内基因组的保守性和变异性。我们还确定了与M. kubicae 的耐药性、毒力和持久性有关的基因 染色体和质粒。M. kubicae基因组和质粒中编码的毒力因子为研究机会性环境 NTM 如何导致疾病奠定了基础。