2020年春天在意大利的医院细菌病原体的泛病原体深度测序:一个前性队列研究
Harry A Thorpe1, Maiju Pesonen1, Marta Corbella2
1Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
The Lancet. Microbe
|August 23, 2024
概括
一种新的细菌深度测序方法在COVID-19大流行期间有效跟踪了医院获得的感染. 这种方法有助于了解病原体的传播,并改善医疗机构的感染控制.
科学领域:
- 微生物学 微生物学
- 基因组学就是基因组学.
- 传染性疾病 传染性疾病
背景情况:
- 鼻腔感染构成重大威胁,特别是在重症监护室 (ICU).
- 随着COVID-19大流行的激增,感染控制措施变得更加紧张,病原体传播风险增加.
- 与医院相关的细菌是流行性的,对敏感患者构成相当大的风险.
研究的目的:
- 评估高患者负担期间医院病原体传播的风险和程度.
- 开发和评估一种新的细菌泛病原体深度测序方法,用于临床监测.
- 为了加强感染控制,将深度测序与标准临床工作流程相结合.
主要方法:
- 在第一个COVID-19浪潮期间,意大利北部的前性队列研究.
- 从住院患者的呼吸道,鼻腔和直肠样本培养的细菌病原体.
- 使用大量深度测序,mSWEEP,mGEMS,snippy,ARIBA和CARD来检测病原体和抗菌素耐药性基因.
主要成果:
- 检测到一个庞大而多样化的病原体种群,在256名患者中检测到2148种病原体.
- 确定了抗微生物耐药性基因的高患病率,包括卡巴酶和扩展谱β-乳糖酶.
- 已建立的医院传播作为主要病原体物种使用高分辨率绘图的重要获取方式.
结论:
- 基于培养的深度测序方法可以改善未来的医院病原体监测和感染控制.
- 该研究表明,深度测序分辨率相当于Acinetobacter baumannii的单个殖民地测序.
- 需要进一步的研究来比较深度测序的准确性,成本和可行性与单个殖民地全基因组测序.
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