The Molecular Epidemiology Program uses pathogen genome sequence data to track how diseases spread and to guide public health responses in Washington.
Program Overview
In public health, many epidemiologists specialize in particular diseases. Molecular epidemiologists, however, specialize in a particular method of analysis. Specifically, we use pathogen genomic data to study many different pathogens.
By analyzing patterns in pathogen genome sequences — the DNA or RNA “blueprints” of organisms that cause disease — we can understand how infections move between people and communities. This modern approach adds a powerful layer of information to traditional public health tools, helping us detect outbreaks, track transmission, and monitor emerging threats in real time.
Integrating molecular data into public health requires collaboration across disciplines.
The Molecular Epidemiology Program works closely with microbiologists, bioinformaticians, and data scientists at the Washington State Department of Health (DOH) to transform pathogen genomic data into actionable insights. Our team designs and evaluates systems for generating genomic data, analyzes those data to uncover patterns of disease transmission, and reports our findings to public health partners and the public.
How are pathogen genomic data helpful in Public Health?
Identifying outbreaks
Comparing pathogen genomes helps us see if infections are - or aren’t - closely related. By determining relationships between infections and looking at who the pathogens were sampled from, it's easier to detect when an outbreak is occurring and which cases are a part of an outbreak.
Tracking lineages and monitoring trends
Genomic data allows us to classify a pathogen into subgroups, or lineages, that we can monitor over time. These categorizations help us watch which lineages are growing or declining. Patterns of growth and decline can warn us about potential public health issues we should address proactively.
Understanding clinical presentation or pathogen characteristics
In some cases, genomic data can tell us something about the clinical presentation of the disease. For example, some genomic changes will make a bacterial infection resistant to antibiotics. In other cases, genomic changes can make a pathogen behave differently, such as spreading between people more easily. When this happens, detecting these genomic patterns can help us understand how to treat or respond to the disease more effectively.
Program Aims
The Molecular Epidemiology Program aims to:
- Expand the generation and collection of pathogen genomic data across Washington by partnering with subject matter experts and external collaborators to design and coordinate genomic surveillance programs.
By strengthening statewide genomic surveillance capacity, we help ensure that Washington can detect and respond to new and emerging pathogens more quickly.
- Increase the use of genomic data to enhance situational awareness and outbreak response. We conduct analyses that support routine surveillance and outbreak response for viral, bacterial, and mycotic notifiable conditions, and we collaborate on genomic analysis of wastewater samples — an early indicator of community-level disease trends.
These analyses help identify outbreaks earlier, guide control measures, and inform data-driven public health decisions.
- Empower other epidemiologists to use genomic data confidently by providing training, consultation, and educational resources.
Building this expertise across programs strengthens the overall public health workforce and promotes consistent, evidence-based use of pathogen genomic data statewide.
Northwest Pathogen Genomics Center of Excellence
We lead one of five CDC-funded Pathogen Genomics Centers of Excellence (PGCoE) in the United States — a national network advancing the use of pathogen genomics in public health practice.
Our Center brings together:
- Epidemiologists at the Washington State Department of Health and Public Health – Seattle & King County
- Microbiologists and bioinformaticians at the Washington State Public Health Laboratory
- Academic researchers at the University of Washington and Fred Hutchinson Cancer Center
- Training and education specialists at the Northwest Center for Public Health Practice
- Veterinary and zoonotic disease experts at the Washington Animal Disease Diagnostic Laboratory at Washington State University
Through this collaboration, we strengthen Washington’s capacity to detect, investigate, and respond to infectious disease threats by translating state-of-the-art approaches in pathogen genomics from academia into public health practice.
To learn more, please visit https://nwpage.org/
Resources
- Introductory reading: For a general overview of how genomic data are used in public health, visit the CDC’s Advanced Molecular Detection website.
- Viral genomic surveillance: We maintain publicly available Nextstrain builds that contextualize viral diversity from Washington alongside national and global data.
- Bacterial and mycotic genomic surveillance: Our surveillance approach integrates genomic cluster detection with traditional epidemiologic methods. Contact us to learn more about this reporting system.
- Educational materials: We offer three publicly available online courses covering the principles of genomic epidemiology, bacterial genomics, and viral genomics.
- Applied public health research: Our team conducts applied genomic epidemiology research and publishes findings in peer-reviewed journals to advance the field.
- Further reading: Explore the Applied Genomic Epidemiology Handbook to dive deeper into genomic epidemiology methods and applications.
Contact us
Email the Molecular Epidemiology program for more information (wgs-epi@doh.wa.gov).
Washington residents or healthcare providers should contact their local health jurisdictions for assistance.