MicrobeTrace: Retooling molecular epidemiology for rapid public health response.

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,...

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Autores principales:	Ellsworth M Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, Sergey Knyazev, Roxana Cintron, William M Switzer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b0d84b739f454fc3a09ba949f1f97896
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spelling	oai:doaj.org-article:b0d84b739f454fc3a09ba949f1f978962021-11-25T05:40:33ZMicrobeTrace: Retooling molecular epidemiology for rapid public health response.1553-734X1553-735810.1371/journal.pcbi.1009300https://doaj.org/article/b0d84b739f454fc3a09ba949f1f978962021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009300https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Outbreak 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.Ellsworth M CampbellAnthony BoylesAnupama ShankarJay KimSergey KnyazevRoxana CintronWilliam M SwitzerPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 9, p e1009300 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Ellsworth M Campbell Anthony Boyles Anupama Shankar Jay Kim Sergey Knyazev Roxana Cintron William M Switzer MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
description	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.
format	article
author	Ellsworth M Campbell Anthony Boyles Anupama Shankar Jay Kim Sergey Knyazev Roxana Cintron William M Switzer
author_facet	Ellsworth M Campbell Anthony Boyles Anupama Shankar Jay Kim Sergey Knyazev Roxana Cintron William M Switzer
author_sort	Ellsworth M Campbell
title	MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
title_short	MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
title_full	MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
title_fullStr	MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
title_full_unstemmed	MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
title_sort	microbetrace: retooling molecular epidemiology for rapid public health response.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/b0d84b739f454fc3a09ba949f1f97896
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MicrobeTrace: Retooling molecular epidemiology for rapid public health response.

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