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牛津纳米孔的2024测序技术用于Listeria monocytogenes疫情检测和来源归因:进展和克隆特异性挑战

Michael Biggel¹, Nicole Cernela¹, Jule Anna Horlbog²

¹Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland.

Journal of clinical microbiology

|October 4, 2024

概括

牛津纳米孔技术 (ONT) 测序显示出对病原体监测的希望,大多数Listeria monocytogenes基因组为高分辨率基因型定型提供了准确的结果. 然而,特定的甲基化模式可能会导致错误,需要进一步改进以检测常规爆发.

科学领域:

基因组学和生物信息学
微生物病原和免疫学
食品安全与公共卫生问题

背景情况:

全基因组测序对于病原体监测和疫情检测至关重要.
牛津纳米孔技术 (ONT) 为无缺口的基因组组装提供了成本效益高,可访问的测序替代方案.
由于最近的技术进步,正在解决对病原体传播研究的ONT准确性的先前限制.

研究的目的:

评估ONT测序对病原体爆发检测的准备程度.
评估ONT-only基因组组合的准确性,用于对Listeria monocytogenes*进行高分辨率的基因型鉴定.
识别导致ONT数据中的序列错误的因素.

主要方法:

使用ONT的V14快速条形码套件和R10.4.1流细胞测序了78个*Listeria monocytogenes*分离物.
采用并测试了几种生物信息工作流程,以优化组装精度.
将来自ONT-only组件的cgMLST配置文件与来自Illumina测序数据的配置文件进行比较.

主要成果:

优化的ONT工作流产生了每个基因组中位数为1个错误 (SNP或indel) 的组件.
来自单 ONT 组件的 cgMLST 档案与 78 个分离物中的 66 个 Illumina 数据相匹配.
八个组件显示了>20个错误,主要与GAAGAC甲基化动机相关,影响了孤立集群.

结论:

大多数使用ONT数据组装的Listeria monocytogenes基因组都适合用于高分辨率的基因型鉴定.
确定GAAGAC甲基化动机是错误的重要来源,影响了遗传学准确性.
为了在疫情爆发和食品安全调查中可靠的常规使用,需要进一步改进ONT化学或基调器.

关键词:

李斯特里亚单细胞原生菌 (Listeria monocytogenes) 是一种牛津纳米孔测序的测序基因组流行病学基因组流行病学甲基转移酶是一种甲基转移酶.疫情爆发的检测和检测.来源归因来源归因进行全基因组测序.

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