MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response

Abstract

MotivationOutbreak 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.ResultsWe developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. Using publicly available HIV sequences and other 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.Availability and ImplementationMicrobeTrace 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. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. The source code is available at https://github.com/cdcgov/microbetrace.Contactells@cdc.gov

Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters

“…The resulting hierarchical tree was visualised using the R package 'ggtree'. The un-clustered matrix was also visualised using MicrobeTrace (https://github.com/CDCgov/MicrobeTrace) [16].…”

Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in Bulgaria

“…Identification of CRF01_AE clusters and characterization of the transmission network was done using the sequence alignment and MicrobeTrace (http://github.com/cdcgov/ microbetrace) [25] at Tamura-Nei genetic distance (d) cutoffs of 0.005 (0.5%), 0.015 (1.5%), and 0.035 (3.5%) nucleotide/substitutions/site. Graphically, transmission linkages are represented by lines drawn between both nodes, where each node represents a participant's pol sequence.…”

Applying Genomic Epidemiology to Characterize a COVID-19 Outbreak in a Developmentally Disabled Adult Group Home Setting, Arizona

“…To further characterize and understand the dynamics of this outbreak, a potential transmission network was developed using MicrobeTrace ( 16 ), which incorporates person-place linkages of all 42 positive cases ascertained through public health investigations and contact tracing ( Figure 2 ). The timeline of the network relies on the earliest collection dates for the positive case samples.…”

“…Staff and resident cases were loaded into MicrobeTrace ( 16 ) as a “Node List” and connections to their respective facilities were loaded as a “Link List” in comma-separated formats. Once loaded in MicrobeTrace: (1) node shapes were mapped to a column distinguishing between persons and places, (2) node labels were mapped to a column populated with a deidentified location ID for all locations, while this column remains empty for all nodes representing persons, (3) node colors were mapped to a column describing the patient outcome, (4) the timeline feature was controlled using the sample collection date as input from the “Node List” file, and finally (5) the graphic was exported as SVG objects at each time interval of interest.…”