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Christine Thomas^1,2, Hanka Brangsch¹, Valentina Galeone³

¹Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743, Jena, Germany.

|August 28, 2025

概括

细菌基因组的纳米孔测序显示了不同物种的组装质量. 虽然一些病原体产生了完美的基因组,但核心基因组MLST位置的错误可能会影响疫情分析的可靠性.

科学领域:

基因组学
生物信息学
微生物致病性

背景情况:

全基因组测序和生物信息学对于细菌基因组探索和疫情分析至关重要.
高度的测序精度和精确的基因组组合对于可靠的基因类型和遗传标记检测至关重要.

研究的目的:

评估牛津纳米孔技术 (ONT) R10.4.1测序对于具有低突变率的高度致病性细菌的基因型的有用性.
评估不同的组装策略及其对基因组准确性的影响.

主要方法:

使用ONT R10.4.1化学和Illumina对六种参考细菌菌株进行测序.
评估各种组装策略与RefSeq组装作为基本真相.
对关键细菌病原体的公开测序数据进行分析.

主要成果:

组装质量因物种而异;Bacillus anthracis实现了近乎完美的组装,而Brucella spp. 显示出核酸的差异.
获得了Klebsiella variicola,Listeria spp.,Mycobacterium tuberculosis,Staphylococcus aureus和Streptococcus pyogenes的完美基因组,这些基因组的基因组组分别是:
特别是在编码序列和甲基化相关的错误被观察到,尽管甲基化意识模型显示了改善. 核心基因组多部位序列类型 (cgMLST) 显示了一些物种的小等位基因差异.

结论:

病原细菌的纳米孔测序数据组合质量取决于物种和方法.
尽管在组件中存在持续的错误,包括cgMLST位点,但特定的工具组合可以在没有短读抛光的情况下产生完美的基因组.

关键词:

组装管道细菌疫情分析牛津纳米孔技术病原体

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