从全基因组测序数据中 in silico 预测的 Mycobacterium 结核病 spoligotypes 和 lineages 的比较
Gary Napier1, David Couvin2, Guislaine Refrégier3,4
1Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
Scientific reports
|July 13, 2023
概括
结合型化和全基因组测序 (WGS) 都可以识别Mycobacterium结核病菌株类型. 虽然spoligotyping与主要血统保持一致,但其准确性在更细微的子血统水平上下降,支持其用于监视的用途.
科学领域:
- 传染病的分子流行病学.
- 对Mycobacterium结核病菌的基因组监测
背景情况:
- 在Mycobacterium结核综合体 (MTBC) 内的细菌菌株类影响结核病 (TB) 疾病特征,包括耐药性,传染性和毒性.
- 杂型化是MTBC菌株鉴定的传统基因型化方法,而全基因组测序 (WGS) 则可以根据SNP进行子系的分类.
- 了解这些基因定型方法之间的一致性对于准确的结核病监测和研究至关重要.
研究的目的:
- 开发和验证一个 in silico spoligotype预测工具,Spolpred2,集成到TB-Profiler.
- 评估MTBC分离物的大数据集中基于spoligotyping和基于SNP的子系谱赋值之间的一致性.
- 为结核病研究和公共卫生中的不同解决需求提供基因型鉴定方法的适当使用指导.
主要方法:
- 开发"Spolpred2",一种用于预测 spoligotypes 的 in silico 方法.
- 将Spolpred2集成到TB-Profiler软件中.
- 对超过28000个MTBC分离物产生血统和spoligotype预测,并对菌株类型重叠的表征.
主要成果:
- 确定的主要聚类型家族包括北京 (25.6%),T (18.6%),LAM (13.1%),CAS (9.4%) 和EAI (8.3%),与已知的地理分布基本一致.
- 大多数spoligotypes和主要的MTBC系 (L1-L7,以及动物) 之间观察到很高的相关性.
- 在较低的等级层次上,一致性下降,只有65%的spoligotypes完全匹配第二层次以外的子系.
结论:
- 无论是基于膜的还是由WGS衍生而来的合型,都适合于结核病的低分辨率流行病学监测.
- 全基因组测序 (WGS) 或基于SNP的类型化方法被推用于需要详细的子系区分的高分辨率研究.
- 这些发现支持基于结核病控制所需的遗传分辨率水平的不同基因定型技术的互补使用.
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