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快速直观病原体监测 (RIPS):一种用于监测来自食物传播细菌病原体的基因组序列数据的工具

Tim Muruvanda¹, Hugh Rand¹, James Pettengill¹

¹Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States.

Frontiers in bioinformatics

|August 26, 2024

概括

快速直观病原体监测 (RIPS) 工具通过可视化全基因组测序数据来增强病原体检测. 这个工具有助于实时监测疫情,使用NCBI病原体检测数据库.

科学领域:

微生物学微生物学
生物信息学是一种生物信息学.
公共卫生公共卫生

背景情况:

国家生物技术信息中心 (NCBI) 病原体检测数据库收集了食物传播病原体的全基因组序列,如Listeria monocytogenes,Salmonella enterica和Escherichia coli.
监测这些数据对于识别新出现的疫情至关重要.
目前的分析结果可以在文本文件中获得,但解释和上下文化具有挑战性.

研究的目的:

开发一种易于使用的工具,用于实时监测病原体基因组序列数据库.
提高病原体监测数据的可访问性和可解释性.

主要方法:

快速直观病原体监测 (RIPS) 工具的开发.
整合全基因组多部位序列类型化 (wgMLST) 数据和来自NCBI数据库的集群结果.
数据以图形,交互式仪表板格式呈现,包括相关元数据.

主要成果:

该RIPS工具有效地显示NCBI快速报告数据.
交互式仪表板有助于对复杂的基因组监测信息进行上下文化和解释.
RIPS增强了病原体基因组序列数据库的实用性,用于实时监控.

结论:

该RIPS工具显著提高了病原体监测数据的可用性.
基因组数据实时可视化有助于更快地检测和应对疫情爆发.
RIPS使公共卫生专业人员能够从大规模的基因组数据集中获得可操作的见解.

关键词:

埃舍里希亚大肠杆菌 (Escherichia coli) 是一个大肠杆菌.李斯特里亚单细胞原生菌 (Listeria monocytogenes) 是一种沙门氏菌 (Salmonella enterica) 已经成为一种常见的疾病.流行病学监测流行病学监测食品安全食品安全通过食物传播的病原体疫情爆发的检测和检测.进行全基因组测序.

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