Singh Kamal, Vijayakumar Saravanan, Sharma Swati, Anupurba Shampa
Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India; Department of Virology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India.
Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India; Statistics Division, ICMR-National Centre for Disease Informatics, Bengaluru, India.
Indian J Med Microbiol. 2025 Jul-Aug;56:100895. doi: 10.1016/j.ijmmb.2025.100895. Epub 2025 Jun 11.
Drug-resistant tuberculosis (DR-TB) presents a formidable public health challenge worldwide. Therefore, this study was conducted to elucidate the complete genetic profiles of drug-sensitive (DS), and drug-resistant TB isolates using Whole Genome Sequencing (WGS).
The study includes a set of sputum specimens containing five DS-TB, multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) from distinct individuals. The identification and susceptibility was confirmed using GeneXpert assay, GenoType MTBDR plus assay, and GenoTypeMTBDRsl assay. Furthermore, specimens were cultured using the BD BACTEC MGIT 960 and subsequently confirmed through Capilia rapid kit. WGS was employed for the identification of Single Nucleotide Polymorphisms (SNPs), Mycobacterium tuberculosis complex (MTBC) lineages, and spoligotypes. The H37Rv was used as a positive control.
The findings of WGS showed, all the MDR-TB and XDR-TB isolates exhibited non-synonymous mutation (Ser450Leu, Gln432Leu, and His445Gln) within the rpoB gene. The isolates were simultaneously harboring mutations at fabG1-8T > C, fabG1-17G > T, fabG1-15C > T, and inhA-154G > A. One DS-TB isolate was carrying resistance mutations in the rrs gene at position 517C > T, while three MDR-TB isolates turned out to be pre-XDR-TB carrying mutations associated with fluoroquinolone (FQ) resistance (gyrA Ala90Val, gyrA Asp94His, and gyrA Asp94 Gly). The study reports novel mutations pncA391dupG and for the first time mutation in thyX gene in clinical isolates of MTBC. Most of the MDR/XDR-TB isolates were predominantly associated with the Beijing sub-lineage within the East Asian Lineage 2.
In conclusion, our study highlighted the challenges surrounding the rapid identification and essential information regarding the genetic diversity of TB strains which contribute valuable insights into the TB epidemiology.
耐多药结核病（DR-TB）在全球范围内构成了严峻的公共卫生挑战。因此，本研究旨在利用全基因组测序（WGS）阐明药物敏感（DS）和耐药结核分枝杆菌分离株的完整基因图谱。
该研究纳入了一组痰液标本，这些标本来自不同个体，包含5株DS-TB、耐多药结核病（MDR-TB）和广泛耐药结核病（XDR-TB）。使用GeneXpert检测、GenoType MTBDR plus检测和GenoTypeMTBDRsl检测来确认鉴定结果和药敏情况。此外，标本采用BD BACTEC MGIT 960进行培养，随后通过Capilia快速试剂盒进行确认。WGS用于鉴定单核苷酸多态性（SNP）、结核分枝杆菌复合群（MTBC）谱系和间隔寡核苷酸分型。H37Rv用作阳性对照。
WGS结果显示，所有MDR-TB和XDR-TB分离株在rpoB基因内均表现出非同义突变（Ser450Leu、Gln432Leu和His445Gln）。这些分离株同时在fabG1-8T>C、fabG1-17G>T、fabG1-15C>T和inhA-154G>A位点发生突变。1株DS-TB分离株在rrs基因的517C>T位点携带耐药突变，而3株MDR-TB分离株被证明是携带与氟喹诺酮（FQ）耐药相关突变（gyrA Ala90Val、gyrA Asp94His和gyrA Asp94Gly）的准广泛耐药结核病（pre-XDR-TB）。该研究报告了新的突变pncA391dupG，并首次报道了MTBC临床分离株中thyX基因的突变。大多数MDR/XDR-TB分离株主要与东亚谱系2中的北京亚谱系相关。
总之，我们的研究突出了围绕快速鉴定以及结核菌株遗传多样性基本信息的挑战，这些信息为结核病流行病学提供了有价值的见解。
