Foundations I: Conceptual Foundations of Pathogen Genomics
- Continuing Education
Registration will open in late January 2026.
Discover how pathogen genomics informs public health decisions and practice.
- Online; Self-Paced
This course is offered on demand and participants progress through the materials at their own pace.
$1
This course is offered for free.
Continuing Education
2 Hours
On This Page
Overview
Foundations I: Conceptual Foundations of Pathogen Genomics introduces learners to the essential concepts underlying this rapidly advancing field. This course provides an overview of pathogen genomics and its transformative role in public health. You will explore foundational concepts in genomics, practical applications, and the key considerations needed to implement effective genomic programs.
The course examines what pathogen genomics is, how it is reshaping our understanding and management of infectious diseases, and highlights the ways in which genomic information is applied in real-world infectious disease investigations—from tracking familiar threats to identifying novel outbreaks. It also explores the expertise and considerations critical to designing adaptable programs that support effective infectious disease response.
Key concepts are presented in brief, accessible video segments, with assessments throughout that allow you to check your understanding and apply your learning. With a focus on conceptual understanding and core principles, this course prepares learners to approach pathogen genomics with confidence as the field continues to evolve and shape public health practice.
Learning Objectives
- Explain what pathogen genomics is and describe how it contributes to public health decision-making.
- Identify common applications of pathogen genomics in public health practice.
- Describe the expertise and key considerations needed to develop and maintain adaptable pathogen genomic programs.
Who Should Enroll?
Foundations I: Conceptual Foundations of Pathogen Genomics is open to any registrant and recommended for anyone involved in infectious disease surveillance or outbreak response, as well as those in adjacent fields who would benefit from understanding the growing role of pathogen genomics in applied public health.
Completion of Foundations I is recommended before taking Foundations II and subsequent courses in this program.
Course topics
Course Introduction
- Voices from the Field: Welcome
- Outbreak in Sunnyport: Using Pathogen Genomics to Help Stop an Infectious Disease
What is Pathogen Genomics?
- Lesson Introduction
- A History of Pathogen Genomics Part I: The Roots of Molecular Epidemiology
- A History of Pathogen Genomics Part II: The Molecular Epidemiology Toolbox
- What's in a Genome? Tracing Pathogen Outbreaks Through DNA
- Scaling Up Pathogen Genomics for Public Health Impact
- Voices from the Field: Origin Stories
Applications of Pathogen Genomics for Public Health
- Lesson Introduction
- Pathogen Characterization: What’s Causing Disease?
- Surveillance Applications: Evaluating Population-Level Trends
- Outbreak Investigations: Decoding the Chain of Transmission
- Pathogen Genomics for Public Health: Key Takeaways
- Voices from the Field: Pathogen Genomics in Action
Implementing Pathogen Genomics for Public Health
- Lesson Introduction
- The ABCs of Generating ACTGs
- Voices from the Field: Working Together for Greater Impact
- Key Considerations for Turning Sequence Data into Public Health Action
- Here to Stay: Building Sustainable Pathogen Genomics Programs
- Pathogen Genomics in Practice: Key Takeaways
- Voices from the Field: The Future
Acknowledgments
These courses were developed under the U.S. Pathogen Genomics Centers of Excellence (PGCoE), and supported by the Office of Advanced Molecular Detection, U.S. Centers for Disease Control and Prevention (CDC) through Cooperative Agreement Number CK22-2204. Contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention.
Course Directors
Shirlee Wohl
PhD
- Project Director, New England Pathogen Genomics Center of Excellence, Massachusetts Department of Public Health
- Lead Investigator, Brigham and Women’s Hospital, Harvard Medical School
Arianna Miles-Jay
PhD, MPH
- Genomic Analysis Unit Manager, Genomics Section, Division of Infectious Diseases, Bureau of Laboratories, Michigan Department of Health and Human Services
“I cannot overstate how impressive I found the quality of this course. Organization, content, aesthetics, and delivery—all were remarkable…. This feels like a very empowering resource, and I believe it will energize and strengthen the public health community.”