Software:Microbetrace

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Microbetrace
Developer(s)Centers for Disease Control and Prevention Division of HIV/AIDS Prevention
Initial releaseJuly 1, 2017; 8 years ago (2017-07-01)
Repositorygithub.com/CDCgov/MicrobeTrace/
Written inTypeScript
PlatformWeb
TypeEpidemiology
LicenseApache License 2.0
Websitemicrobetrace.cdc.gov

MicrobeTrace is an open-source, browser-based software platform developed by the Centers for Disease Control and Prevention (CDC) for the visualization and analysis of molecular epidemiology and transmission networks of infectious diseases.[1]

The platform enables integration of pathogen genetic sequence data with epidemiologic and demographic information to support analysis in outbreak investigations and public health research.[2]

Functionality

MicrobeTrace provides interactive tools for visualization of transmission networks derived from genetic distance data, phylogenetic tree exploration, and integration of molecular, demographic, and epidemiologic datasets. The platform also supports temporal and geospatial analysis of infectious disease outbreaks. Because it operates within a web browser, analyses can be conducted locally without requiring external data upload.[3]

Applications

MicrobeTrace has been applied in studies of multiple infectious diseases across diverse geographic settings, including viral, bacterial, and parasitic pathogens.[4]

HIV

The platform has been used in molecular epidemiology studies of HIV transmission, including outbreak investigations among people who inject drugs in the United States and analyses of transmission dynamics in international settings.[5][6][7]

Viral hepatitis

MicrobeTrace has been used in genomic epidemiology investigations of hepatitis A and hepatitis C, including outbreak detection and transmission analysis in both community and institutional settings.[8][9]

Bacterial and parasitic diseases

The software has also been applied in studies of bacterial and parasitic pathogens, including analyses of transmission dynamics of Neisseria gonorrhoeae, tuberculosis outbreak investigations, and genotyping of Cyclospora cayetanensis clusters.[10][11][12]

Respiratory viruses

During the COVID-19 pandemic, MicrobeTrace was used in outbreak investigations in community and institutional settings, including studies of transmission associated with social events and university populations.[13][14]

Other pathogens

The platform has also been applied to emerging infectious diseases, including investigations of mpox transmission.[15]

Availability

MicrobeTrace is distributed as open-source software and is available through the CDC's public code repository. It is designed to run in modern web browsers without requiring installation.[16]

See also

References

  1. ↑ Campbell, EM (2021). "MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response". PLOS Computational Biology 17 (9). doi:10.1371/journal.pcbi.1009300. PMID 34492010. Bibcode: 2021PLSCB..17E9300C. 
  2. ↑ Shankar, A (2025). "MicrobeTrace 2.0: The enhanced visualization multitool for molecular epidemiology and bioinformatics". Molecular Biology and Evolution 43. doi:10.1093/molbev/msaf334. PMID 41479018. 
  3. ↑ Campbell, EM (2021). "MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response". PLOS Computational Biology 17 (9). doi:10.1371/journal.pcbi.1009300. PMID 34492010. Bibcode: 2021PLSCB..17E9300C. 
  4. ↑ "Cited In for PMID: 34492010 - Search Results - PubMed" (in en). https://pubmed.ncbi.nlm.nih.gov/?linkname=pubmed_pubmed_citedin&from_uid=34492010. 
  5. ↑ Tumpney, M (2020). "HIV Outbreak Investigation among Persons Who Inject Drugs in Massachusetts Enhanced by HIV Sequence Data". Journal of Infectious Diseases 222 (Suppl 5): S259–S267. doi:10.1093/infdis/jiaa053. PMID 32877558. 
  6. ↑ Taiaroa, G (2024). "Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study". The Lancet Regional Health – Western Pacific 47. doi:10.1016/j.lanwpc.2024.101103. PMID 38953059. 
  7. ↑ Brenner, BG (2021). "The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020)". Viruses 13 (8): 1643. doi:10.3390/v13081643. PMID 34452506. 
  8. ↑ Doyle, TJ (2025). "Genomic Epidemiology of Resurgent Hepatitis A in Florida, 2018–2022". Journal of Infectious Diseases 232 (4): 943–952. doi:10.1093/infdis/jiaf127. PMID 40066809. 
  9. ↑ Walsh, KB (2025). "Hepatitis C Outbreak Identification and Response in a High-Security Unit Within a California County Jail". Journal of Correctional Health Care 31 (5): 282–289. doi:10.1177/10783458251380106. PMID 40971290. 
  10. ↑ Town, K (2020). "Phylogenomic analysis of Neisseria gonorrhoeae transmission to assess sexual mixing and HIV transmission risk in England". The Lancet Infectious Diseases 20 (4): 478–486. doi:10.1016/S1473-3099(19)30610-3. PMID 31978353. 
  11. ↑ Labuda, SM (2022). "Tuberculosis Outbreak Associated With Delayed Diagnosis and Long Infectious Periods in Rural Arkansas, 2010–2018". Public Health Reports 137 (1): 94–101. doi:10.1177/0033354921999167. PMID 33729050. 
  12. ↑ Barratt, J (2022). "Genotyping Cyclospora cayetanensis From Multiple Outbreak Clusters With An Emphasis on a Cluster Linked to Bagged Salad Mix—United States, 2020". Journal of Infectious Diseases 225 (12): 2176–2180. doi:10.1093/infdis/jiab495. PMID 34606577. 
  13. ↑ Mahale, P.; Rothfuss, C.; Bly, S.; Kelley, M.; Bennett, S.; Huston, S. L.; Robinson, S. (2020). "Multiple COVID-19 outbreaks linked to a wedding reception in rural Maine". MMWR Morb Mortal Wkly Rep 69 (45): 1686–1690. doi:10.15585/mmwr.mm6945a5. PMID 33180752. 
  14. ↑ Doyle, K.; Teran, R. A.; Reefhuis, J.; Kerins, J. L.; Qiu, X.; Green, S. J.; Choi, H.; Madni, S. A. et al. (2021). "Multiple Variants of SARS-CoV-2 in a University Outbreak After Spring Break — Chicago, Illinois, 2021". MMWR Morb Mortal Wkly Rep 70 (35): 1195–1200. doi:10.15585/mmwr.mm7035a3. PMID 34473687. 
  15. ↑ Ortiz, Nancy; Rodriguez, Luis R.; McPherson, Mecca; Pringle, Kristen; Rao, Agam K.; Tuttle, Alexandra; Hughes, Christine M.; Kachur, Rachel E. et al. (2025). "Clade II Mpox infections among cruise ship passengers and crew members — United States, 2024". MMWR Morb Mortal Wkly Rep 74 (22): 373–378. doi:10.15585/mmwr.mm7422a1. PMID 40531694. 
  16. ↑ CDCgov/MicrobeTrace, Centers for Disease Control and Prevention, 2026-03-27, https://github.com/CDCgov/MicrobeTrace, retrieved 2026-03-30 

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