| 项目编号 | PRJCA030108 | ||||||||||||||||||||||||||||||||||||||||
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| 项目标题 | Whole genome sequencing reveals transmission pattern and drug resistance of Mycobacterium tuberculosis intra- or inter-hosts | ||||||||||||||||||||||||||||||||||||||||
| 涉及领域 | Medical | ||||||||||||||||||||||||||||||||||||||||
| 数据类型 | Whole genome sequencing | ||||||||||||||||||||||||||||||||||||||||
| 物种名称 |
Mycobacterium tuberculosis
Mycobacterium kansasii Mycobacteroides abscessus Mycobacterium intracellulare Mycobacterium gordonae |
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| 描述信息 | This study aimed to investigate the transmission pattern of Mycobacterium tuberculosis complex (MTBC) in Shenzhen, China. We conducted a retrospective study on 286 samples form 184 TB patients collected between 2015 and 2018 using WGS. Drug susceptibility testing (DST) was performed using both culture-based phenotypic DST (pDST) and genotyping-based molecular DST (mDST). Sample diversity was evaluated by SNPs and transmission clusters were identified based on SNP differences of 12 or fewer in the node of the phylogenetic tree. The overall multidrug-resistant (MDR) rate was 22.31% in pDST (12.00% for new patients and 40.82% for retreatment patients) and 36.78% in mDST (24.49% for new patients and 58.21% for retreatment patients). A total of 92 transmission clusters were identified, encompassing 70.21% samples (57.46% patients), with 5 clusters (5.43%) contained samples from different patients, indicating recent transmission of MTBC strains. The drug resistant mutations in 36 of 45 transmission clusters (80.00%) were completely consistent in all samples, suggesting the transmission of drug resistant. Patients with multiple samples were categorized into simultaneous sampling (SS) and continuous sampling (CS) groups, revealing significant differences in treatment types, treatment outcomes, residential addresses, and drug resistance types. mDST showed greater accuracy than pDST in SS and CS groups. A novel method based on heterogeneous SNPs and Two-sample Kolmogorov-Smirnov test were developed and identified 12 (12 patients) of 282 (4.26%) samples as mixed infection samples. 6 of 12 patients had mixed and pure samples together and major strains of mixed samples were closer to corresponding pure strains than minor strains. WGS enabled a detailed analysis of MTBC transmission and drug-resistant mutations intra- or inter-hosts. | ||||||||||||||||||||||||||||||||||||||||
| 样品范围 | Multiisolate | ||||||||||||||||||||||||||||||||||||||||
| 发布日期 | 2025-02-24 | ||||||||||||||||||||||||||||||||||||||||
| 出版信息 |
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| 项目资金来源 |
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| 提交者 | Wanfei Liu (liuwanfei@caas.cn) | ||||||||||||||||||||||||||||||||||||||||
| 提交单位 | Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences | ||||||||||||||||||||||||||||||||||||||||
| 提交日期 | 2024-09-12 |