Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates.
Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates.
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DOI：
10.1099/mgen.0.000497
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发表时间：
2021-01
影响因子：
3.9
通讯作者：
Strong M
中科院分区：
文献类型：
--
作者：
Hendrix J;Epperson LE;Durbin D;Honda JR;Strong M
Kubicae分枝杆菌是近200种非结核分枝杆菌（NTM）中的一种，NTM是环境微生物，在某些情况下可以感染人类并引起严重的肺部，皮肤和软组织感染。尽管许多研究已经调查了流行的临床NTM菌种（包括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菌种（包括分枝杆菌）中存在遗传变异。库比科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调查NTM的致病潜力以及用于诊断方法都很重要，甚至对于不太经常引起人类疾病的物种也是如此。在这里，我们报告了两个M的完整基因组。kubicae菌株，分离自两名无关患者。使用来自Illumina和Oxford Nanopore Technologies平台的序列读段的混合短读段和长读段测序和组装用于解析每个分离株的染色体和质粒序列。NJH_MKUB1的基因组含有5135个编码序列（CDS）、一条长度为5.3Mb的环状染色体和两个质粒。NJH_MKUB2的基因组含有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最近发布的四个M基因组草案进行了比较。kubicae，以便更好地了解种内基因组保守性和变异性。我们还确定了与耐药性、毒力和持久性有关的基因。kubicae染色体和质粒。毒力因子编码于M. kubicae为研究机会性环境NTM如何引起疾病提供了基础。
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.
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DOI：
10.1093/bioinformatics/btx610
发表时间：
2018-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Hadfield J;Croucher NJ;Goater RJ;Abudahab K;Aanensen DM;Harris SR
通讯作者：
Harris SR
影响因子：
56.3
作者：
van Ingen, Jakko;Kohl, Thomas A.;Sax, Hugo
通讯作者：
Sax, Hugo
影响因子：
5.8
作者：
Page, Andrew J.;Cummins, Carla A.;Parkhill, Julian
通讯作者：
Parkhill, Julian
影响因子：
12.3
作者：
Jain M;Olsen HE;Paten B;Akeson M
通讯作者：
Akeson M
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.