Sharma Kusum, Verma Renu, Advani Jayshree, Chatterjee Oishi, Solanki Hitendra S, Sharma Aman, Varma Subhash, Modi Manish, Ray Pallab, Mukherjee Kanchan K, Sharma Megha, Dhillion Mandeed Singh, Suar Mrutyunjay, Chatterjee Aditi, Pandey Akhilesh, Prasad Thottethodi Subrahmanya Keshava, Gowda Harsha
1 Department of Medical Microbiology, PGIMER , Chandigarh, India .
2 Institute of Bioinformatics , International Technology Park, Bangalore, India .
OMICS. 2017 Jul;21(7):413-425. doi: 10.1089/omi.2017.0070.
Tuberculosis (TB) remains one of the leading causes of morbidity and mortality worldwide. Extrapulmonary tuberculosis (EPTB) constitutes around 15-20% of TB cases in immunocompetent individuals. Extrapulmonary sites that are affected by TB include bones, lymph nodes, meningitis, pleura, and genitourinary tract. Whole genome sequencing has emerged as a powerful tool to map genetic diversity among Mycobacterium tuberculosis (MTB) isolates and identify the genomic signatures associated with drug resistance, pathogenesis, and disease transmission. Several pulmonary isolates of MTB have been sequenced over the years. However, availability of whole genome sequences of MTB isolates from extrapulmonary sites is limited. Some studies suggest that genetic variations in MTB might contribute to disease presentation in extrapulmonary sites. This can be addressed if whole genome sequence data from large number of extrapulmonary isolates becomes available. In this study, we have performed whole genome sequencing of five MTB clinical isolates derived from EPTB sites using next-generation sequencing platform. We identified 1434 nonsynonymous single nucleotide variations (SNVs), 143 insertions and 105 deletions. This includes 279 SNVs that were not reported before in publicly available datasets. We found several mutations that are known to confer resistance to drugs. All the five isolates belonged to East-African-Indian lineage (lineage 3). We identified 9 putative prophage DNA integrations and 14 predicted clustered regularly interspaced short palindromic repeats (CRISPR) in MTB genome. Our analysis indicates that more work is needed to map the genetic diversity of MTB. Whole genome sequencing in conjunction with comprehensive drug susceptibility testing can reveal clinically relevant mutations associated with drug resistance.
结核病（TB）仍然是全球发病和死亡的主要原因之一。在免疫功能正常的个体中，肺外结核病（EPTB）约占结核病病例的15%-20%。受结核病影响的肺外部位包括骨骼、淋巴结、脑膜炎、胸膜和泌尿生殖道。全基因组测序已成为一种强大的工具，可用于绘制结核分枝杆菌（MTB）分离株之间的遗传多样性图谱，并识别与耐药性、发病机制和疾病传播相关的基因组特征。多年来，已经对几种MTB的肺部分离株进行了测序。然而，来自肺外部位的MTB分离株的全基因组序列有限。一些研究表明，MTB的基因变异可能导致肺外部位的疾病表现。如果能获得大量肺外分离株的全基因组序列数据，这个问题就能得到解决。在本研究中，我们使用下一代测序平台对来自EPTB部位的5株MTB临床分离株进行了全基因组测序。我们鉴定出1434个非同义单核苷酸变异（SNV）、143个插入和105个缺失。这包括279个之前在公开可用数据集中未报告的SNV。我们发现了几个已知赋予耐药性的突变。所有5株分离株均属于东非-印度谱系（谱系3）。我们在MTB基因组中鉴定出9个推定的原噬菌体DNA整合和14个预测的成簇规律间隔短回文重复序列（CRISPR）。我们的分析表明，需要开展更多工作来绘制MTB的遗传多样性图谱。全基因组测序结合全面的药物敏感性测试可以揭示与耐药性相关的临床相关突变。
