一项实验室间的研究描述了生物信息学方法对以基因组为基础的食物传播细菌病原体集群检测的影响
Leonie F Forth1, Burkhard Malorny1, Markus Bönn2
1Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.
Frontiers in microbiology
|November 19, 2025
概括
食品传播病原体全基因组测序集群的实验室间变异是由生物信息学和质量指标解释驱动的. 标准化协议对于准确的监测和疫情调查至关重要.
科学领域:
- 食品传播病原体监测监测
- 基因组流行病学 基因组流行病学
- 生物信息学是一种生物信息学.
背景情况:
- 准确的全基因组测序 (WGS) 聚类对于食品传播疫情的调查至关重要,但面临着挑战.
- 生物信息学工具和质量指标的可变性对聚类结果产生重大影响.
研究的目的:
- 评估关键的食源性病原体在集群识别中的实验室间差异.
- 评估不同生物信息学协议和质量指标解释对聚类结果的影响.
主要方法:
- 分发了四个原始Illumina配对末端序列的数据集,用于*Escherichia coli*,*Listeria monocytogenes*,*Salmonella enterica*和*Campylobacter jejuni*.
- 参与者应用了公司内部的质量评估协议,7基因MLST,cgMLST和SNP调用.
- 样品被分配到基于等位基距离和突变的集群.
主要成果:
- 原始序列和基因组组装质量解释的差异影响了样本的纳入和集群组成.
- 在样本纳入决策中,物种内污染是变化的主要驱动因素.
- cgMLST的可复制性通常很高,但方案选择对*C. jejuni*的结果产生了重大影响.
- 与Snippy呼叫的SNP是一致的,除了具有重组过的*C. jejuni*.
结论:
- 质量指标的解释和生物信息学工具的选择对疫情调查中的基于WGS的聚类产生了重大影响.
- 标准化协议对于可靠的实验室间比较和强大的食品传播病原体监测至关重要.
- 低分辨率的cgMLST模式对*C. jejuni*是不够的,并且在切线附近的聚类对工具选择很敏感.
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