Center for Papua Health Research and Development, Papua, Indonesia.
Jayapura Regional Health Laboratory, Papua, Indonesia.
BMC Genomics. 2021 Nov 22;22(1):844. doi: 10.1186/s12864-021-08139-3.
Tuberculosis is one of the deadliest disease caused by Mycobacterium tuberculosis. Its treatment still becomes a burden for many countries including Indonesia. Drug resistance is one of the problems in TB treatment. However, a development in the molecular field through Whole-genome sequencing (WGS) can be used as a solution in detecting mutations associated with TB- drugs. This investigation intended to implement this data for supporting the scientific community in deeply understanding any TB epidemiology and evolution in Papua along with detecting any mutations in genes associated with TB-Drugs.
A whole-genome sequencing was performed on the random samples from TB Referral Laboratory in Papua utilizing MiSeq 600 cycle Reagent Kit (V3). Furthermore, TBProfiler was used for genome analysis, RAST Server was employed for annotation, while Gview server was applied for BLAST genome mapping and a Microscope server was implemented for Regions of Genomic Plasticity (RGP). The largest genome of M. tuberculosis obtained was at the size of 4,396,040 bp with subsystems number at 309 and the number of coding sequences at 4326. One sample (TB751) contained one RGP. The drug resistance analysis revealed that several mutations associated with TB-drug resistance existed. In details, mutations of rpoB gene which were identified as S450L, D435Y, H445Y, L430P, and Q432K had caused the reduced effectiveness of rifampicin; while the mutases in katG (S315T), kasA (312S), inhA (I21V), and Rv1482c-fabG1 (C-15 T) genes had contributed to the resistance in isoniazid. In streptomycin, the resistance was triggered by the mutations in rpsL (K43R) and rrs (A514C, A514T) genes, and, in Amikacin, its resistance was led by mutations in rrs (A514C) gene. Additionally, in Ethambutol and Pyrazinamide, their reduced effectiveness was provoked by embB gene mutases (M306L, M306V, D1024N) and pncA (W119R).
The results from whole-genome sequencing of TB clinical sample in Papua, Indonesia could contribute to the surveillance of TB-drug resistance. In the drug resistance profile, there were 15 Multi Drugs Resistance (MDR) samples. However, Extensively Drug-resistant (XDR) samples have not been found, but samples were resistant to only Amikacin, a second-line drug.
结核病是由结核分枝杆菌引起的最致命疾病之一。其治疗仍然是包括印度尼西亚在内的许多国家的负担。耐药性是结核病治疗中的问题之一。然而，通过全基因组测序（WGS）在分子领域的发展可以用于检测与结核病药物相关的突变。本研究旨在将这些数据用于支持科学界深入了解巴布亚的结核病流行病学和进化，并检测与结核病药物相关的基因突变。
对巴布亚结核病参考实验室的随机样本进行了全基因组测序，使用 MiSeq 600 循环试剂盒（V3）。此外，TBProfiler 用于基因组分析，RAST Server 用于注释，而 Gview 服务器用于 BLAST 基因组映射，Microscope 服务器用于基因组可塑性区域（RGP）。获得的最大结核分枝杆菌基因组大小为 4396040bp，亚系统数量为 309，编码序列数量为 4326。一个样本（TB751）含有一个 RGP。耐药性分析显示存在与结核病药物耐药性相关的多种突变。具体来说，rpoB 基因的突变被鉴定为 S450L、D435Y、H445Y、L430P 和 Q432K，导致利福平的疗效降低；而 katG（S315T）、kasA（312S）、inhA（I21V）和 Rv1482c-fabG1（C-15T）基因中的突变导致异烟肼耐药。在链霉素中，rpsL（K43R）和 rrs（A514C、A514T）基因的突变引发了耐药性，而阿米卡星的耐药性则是由 rrs（A514C）基因的突变引起的。此外，在乙胺丁醇和吡嗪酰胺中，embB 基因突变（M306L、M306V、D1024N）和 pncA（W119R）导致其疗效降低。
印度尼西亚巴布亚的结核病临床样本全基因组测序结果有助于监测结核病药物耐药性。在耐药谱中，有 15 例多药耐药（MDR）样本。然而，尚未发现广泛耐药（XDR）样本，但样本仅对阿米卡星（二线药物）耐药。
