湿实验室协议对食品传播微生物病原体全基因组短读序列质量的影响

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Leonie F Forth¹, Erik Brinks², Grégoire Denay³

¹Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.

Frontiers in microbiology

|December 14, 2023

概括

实验室间测序研究揭示了食品传播病原体如大肠杆菌和沙门氏菌的高质量数据. 对于在不同实验室和方法中比较数据,SNP分析比cgMLST更强大.

科学领域:

食品微生物学食品微生物学
基因组测序是指基因组的测序.
生物信息学是一种生物信息学.

背景情况:

揭示食物传播感染链需要高质量的微生物测序数据.
调查通常涉及多个实验室,可能引入可变性.
标准化协议对于微生物污染物的可靠比较分析至关重要.

研究的目的:

评估因不同湿实验室程序而导致的测序数据质量的变化.
为了比较不同测序技术和生物信息学工具的性能.
评估SNP和cgMLST分析对实验室间比较的适用性.

主要方法:

涉及四种主要的食源性病原体的实验室间研究:Campylobacter spp.,生产Shiga毒素的大肠杆菌,Listeria monocytogenes和沙门氏菌.
参与者使用常规的内部协议来对细菌培养物和分离的DNA进行短读测序.
序列和组装质量的集中分析,包括SNP和cgMLST调用;组装器SPAdes和SKESA的比较.

主要成果:

照明测序数据质量通常高,变化很低,除了一个图书馆准备套件外.
离子流数据显示所有测试物种的变异性更高.
对于比较来自不同贡献者的数据,SNP分析比cgMLST更适合,过器减少了技术工件;Campylobacter分离物显示出更高的分歧.

结论:

湿实验室程序可以引入变异性,但对于关键的食源性病原体,可以获得高质量的序列数据.
SNP分析提供了一个比cgMLST更可靠的方法来进行实验室间数据比较.
无论是Illumina还是Ion Torrent平台都能生成有价值的数据,尽管Illumina的变化较小.

关键词:

这是坎比洛巴克特菌.埃斯克里希亚病 (Escherichia) 是一种疾病.李斯特里亚病毒 (Listeria) 是一种沙门氏菌是一种沙门氏菌.实验室间的研究研究.协议协议协议协议协议质量质量质量质量质量质量.整个基因组的测序.

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