Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
Northrup Grumman, Atlanta, Georgia, United States of America.
PLoS Comput Biol. 2021 Sep 7;17(9):e1009300. doi: 10.1371/journal.pcbi.1009300. eCollection 2021 Sep.
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.
暴发调查利用来自访谈、医疗保健提供者、实验室和监测系统的数据。然而，多源数据的综合利用需要使用各种软件，这在可用性、互操作性、保密性和成本方面带来了挑战。快速整合、可视化和分析来自多个来源的数据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中数据集成和探索的障碍，促进快速的公共卫生应对。MicrobeTrace 是一个基于网络的、客户端的、基于 JavaScript 的应用程序（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仍然可以完全运行。我们使用公开可用的数据演示了病毒遗传距离网络的分析，并引入了一种新的最小生成树方法，简化了结果。我们还通过分析和显示 2020 年初韩国 SARS-CoV-2 暴发的数据，说明了 MicrobeTrace 在支持接触者追踪方面的潜在效用。MicrobeTrace 由疾病控制和预防中心开发和积极维护。用户可以通过电子邮件 microbetrace@cdc.gov 获得支持。源代码可在 https://github.com/cdcgov/microbetrace 获得。
