在临床环境中评估牛津纳米孔技术的工作流程,用于临床环境中与疫情相关的细菌分离物的基因组流行病学
Stefan Neuenschwander1, Loïc Borcard1, Sonja Gempeler1
1Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
Microbial genomics
|February 10, 2026
概括
牛津纳米孔技术 (ONT) 的全基因组测序 (WGS) 显示了细菌感染诊断的前景. 只有纳米孔的方法在疫情调查中为细菌类型提供了准确性和一致性.
科学领域:
- 微生物学 微生物学
- 基因组学就是基因组学.
- 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) 对于临床诊断和细菌感染的监测至关重要.
- 牛津纳米孔技术 (ONT) 为快速的细菌WGS提供了潜在的工作流.
研究的目的:
- 评估新的ONT工作流程 (R10.4.1流动细胞,V14 RBK套件) 对临床相关细菌的WGS的性能.
- 将ONT WGS的性能与Illumina MiSeq进行基因组组装,基因型定型和抗菌素耐药性预测.
主要方法:
- 使用ONT和IlluminaWGS,对与疫情相关的*Corynebacterium diphtheriae* (CDIP) 和抗万科胺素的肠球菌 (VRE) 的回顾性分析.
- 基于转移酶 (RBK) 和基于PCR (RPB) 的图书馆准备套件的评估.
- 基因组组装质量,多位置序列类型 (MLST,cgMLST),SNP概况和抗菌素耐药性 (AMR) 预测的基因组组装质量.
主要成果:
- 在经过测试的ONT套件中,与MLST (两种物种) 和cgMLST (CDIP) 的Illumina完全一致.
- 对VRE的cgMLST显示出变异性,但使用最新的基调模型的PCR基套件重现了Illumina的结果.
- 基因组AMR预测在测序方法中一致;混合策略提高了准确性和完整性.
结论:
- 只有ONT测序在疫情调查中提供了细菌类型的准确性和一致性.
- 该研究强调了不同ONT图书馆准备方法的优点和局限性.
- 这表明了纳米孔测序在临床微生物学实验室更广泛采用的潜力.
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