MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
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MicrobeTrace：重组分子流行病学以快速应对公共卫生。
DOI：
10.1371/journal.pcbi.1009300
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发表时间：
2021-09
影响因子：
4.3
通讯作者：
Switzer WM
中科院分区：
文献类型：
--
作者：
Campbell EM;Boyles A;Shankar A;Kim J;Knyazev S;Cintron R;Switzer WM
疫情调查使用来自访谈、医疗保健提供者、实验室和监测系统的数据。然而，集成使用多个来源的数据需要拼凑软件，这在可用性、互操作性、保密性和成本方面提出了挑战。来自多个来源的数据的快速整合、可视化和分析可以指导有效的公共卫生干预措施。我们开发了 MicrobeTrace，通过克服分子流行病学数据整合和探索的障碍，促进快速公共卫生反应。 MicrobeTrace 是一个基于 Web 的客户端 JavaScript 应用程序 (https://microbetrace.cdc.gov)，它在基于 Chromium 的浏览器中运行，并且在没有互联网连接的情况下也能保持完全运行。使用公开数据，我们演示了病毒遗传距离网络的分析，并引入了一种简化结果的最小生成树的新方法。我们还通过分析和显示 2020 年初韩国爆发的 SARS-CoV-2 数据，说明了 MicrobeTrace 在支持接触者追踪方面的潜在效用。MicrobeTrace 由美国疾病控制与预防中心开发并积极维护。用户可以发送电子邮件至 microbetrace@cdc.gov 寻求支持。源代码可在 https://github.com/cdcgov/microbetrace 获取。数据科学和生物信息学领域的快速发展显着改进了公共卫生中使用的分子流行病学工具，并导致疫情调查和病原体传播研究的方式发生重大变化。然而，对专业计算机技能的需求往往阻碍了许多这些工具在公共卫生领域的使用。我们通过开发一种名为 MicrobeTrace 的直观独立工具来弥合这一知识差距，以安全地集成、可视化和探索病原体流行病学数据。 MicrobeTrace 是一种易于使用的基于浏览器的工具，可以有效地将接触者追踪和/或微生物基因组数据与人口统计或行为信息合并，从而形成优雅且信息丰富的网络以及多种可定制的可视化效果。 MicrobeTrace 可以离线使用，并在现场本地执行分析，确保个人身份信息 (PII) 的安全和保密使用。我们提供了如何在公共卫生领域使用 MicrobeTrace 的真实示例，包括 COVID 疫情调查。
Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. We developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. MicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully operational without an internet connection. Using publicly available data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. Users can email microbetrace@cdc.gov for support. The source code is available at https://github.com/cdcgov/microbetrace. Rapid advances in the fields of data science and bioinformatics have significantly improved molecular epidemiology tools used in public health and have led to major changes in the way outbreak investigation and pathogen transmission studies are conducted. However, the need for specialized computer skills often impedes the use of many of these tools in the public heath domain. We bridge this knowledge gap by development of an intuitive, standalone tool called MicrobeTrace to securely integrate, visualize and explore pathogen epidemiologic data. MicrobeTrace is an easy to use browser-based tool which can effectively merge contact tracing and/or microbial genomic data with demographic or behavioral information, resulting in elegant and informative networks as well as multiple customizable visualizations. MicrobeTrace can be used offline, with analyses being performed locally in the field, ensuring secure and confidential use of personally identifiable information (PII). We provide real world examples of how MicrobeTrace has been used in public health, including COVID outbreak investigations.
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DOI：
10.15585/mmwr.mm6948a2
发表时间：
2020-12-04
期刊：
MMWR. Morbidity and mortality weekly report
影响因子：
--
作者：
Center KE;Da Silva J;Hernandez AL;Vang K;Martin DW;Mazurek J;Lilo EA;Zimmerman NK;Krow-Lucal E;Campbell EM;Cowins JV;Walker C;Dominguez KL;Gallo B;Gunn JKL;McCormick D;Cochran C;Smith MR;Dillaha JA;James AE
通讯作者：
James AE
影响因子：
33.9
作者：
Cranston, Kevin;Alpren, Charles;Demaria, Alfred, Jr.
通讯作者：
Demaria, Alfred, Jr.
影响因子：
3.9
作者：
Argimón S;Abudahab K;Goater RJE;Fedosejev A;Bhai J;Glasner C;Feil EJ;Holden MTG;Yeats CA;Grundmann H;Spratt BG;Aanensen DM
通讯作者：
Aanensen DM
影响因子：
3.4
作者：
Fourment M;Gibbs MJ
通讯作者：
Gibbs MJ
影响因子：
6.4
作者：
Campbell, Ellsworth M.;Jia, Hongwei;Switzer, William M.
通讯作者：
Switzer, William M.