Pathogen Genomics for Public Health

Harness the power of pathogen genomics in infectious disease response.

Illustration for Pathogen Genomics for Public Health course.

Pathogens are part of life, responsible for illnesses ranging from the common cold to large-scale outbreaks affecting millions. As infectious diseases continue to evolve, so too must our approaches to surveillance and response. Pathogen genomics offers groundbreaking tools to track how diseases emerge, shift, and spread. By studying the genetic code of disease-causing pathogens, we can identify both new and familiar threats, track their spread, and guide effective public health action.

Build the skills and confidence to turn genomic insights into action with the Pathogen Genomics for Public Health series.

Illustration from Pathogen Genomics for Public Health course.

Foundations I: Conceptual Foundations of Pathogen Genomics

Discover how pathogen genomics informs public health decisions and practice.

Aimed at public health staff, infectious disease professionals, and curious learners alike, this course requires no prior scientific or genomic background. With a focus on conceptual understanding and core principles, this course equips learners with the essential knowledge to understand how pathogen genomics is shaping and advancing public health.

View Course

CDC C2 web image

Foundations II: Technical Introduction to Pathogen Genomic Epidemiology: Mutations, Transmission, and Phylogenetics

Explore how genomic patterns help us understand infectious disease transmission.

This course explores the molecular science that underpins pathogen genomic sequencing. Focusing on scientific principles, this course equips learners with the knowledge needed to inform effective disease surveillance and response in real-world public health contexts.

View Course

Sequencing Strategies Course Icon

Sequencing Strategies for Pathogen Genomics

See how sequencing strategies shape how pathogen genomic data can be used in public health.

Aimed at public health and infectious disease staff who work with public health laboratories, this course provides an overview of common genomic sequencing strategies and library-construction approaches used for public health applications. The course emphasizes key considerations in the sequencing process, including library construction approaches, specimen type and pathogen biology, public health use cases, and practical considerations.

View Course

More Courses Coming Soon

  • Pathogen Genomics for Epidemiology: Planning an Investigation

  • Pathogen Genomics for Epidemiology: Interpretation

Getting Started

  • Current public health workforce
    • Public health agency staff engaged in infectious disease response or biosurveillance, including laboratorians, bioinformaticians, and epidemiologists
    • Professionals supporting infectious disease teams, such as IT leaders, laboratory directors, researchers, and public health administrators
  • Future public health workforce
    • Fellows, students, and trainees in public health, infectious disease epidemiology, biosurveillance, or related programs who want to build a strong foundation in pathogen genomics
  • And more
    • Medical providers, hospital infection preventionists, and others involved in clinical care of infectious disease
    • Researchers working in infectious disease, population health, or tracking biothreats
    • Anyone curious about how pathogen genomics is advancing infectious disease detection, tracking, and response to biothreats
  • Open access and self-paced-study on your schedule
  • Presented by leading experts in pathogen genomics
  • Grounded in real-world examples from public health agencies
  • Fostering a common language and purpose as the field of pathogen genomics evolves

Begin your learning journey

Build the skills to turn genomic data into public health action

Join a community of learners building the skills to turn pathogen genomic insights into effective public health action.

Start with Foundations I, an introduction for anyone in public health or with a general interest in understanding pathogen genomics. In this course, you’ll discover what pathogen genomics is and why it’s becoming an essential tool for tracking infectious diseases and responding to outbreaks.

Continue with Foundations II to deepen your understanding of key principles in molecular biology that underpin genomic epidemiology. You’ll explore how sequencing pathogen genomes can reveal important insights into pathogen transmission—laying the groundwork for more advanced topics in additional courses.

For epidemiologists working with genomic data, continue with the three-course track, Pathogen Genomics for Epidemiology, which includes:

  • Sequencing Strategies
  • Pathogen Genomics for Epidemiology: Planning an Investigation (coming soon)
  • Pathogen Genomics for Epidemiology: Interpretation (coming soon)

Additional courses are planned for 2027 and beyond.

Pathogen Genomics Centers of Excellence Logo.

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. View Full Acknowledgments