Pathogen Genomics Center of Excellence

Background and Purpose

The COVID-19 pandemic highlighted gaps in public health readiness and accelerated the use of genomic surveillance and epidemiology in global health responses. Tools such as microbial sequencing, phylogenetic analysis, and molecular diagnostics are critical for infectious disease preparedness but require specialized expertise. Many public health departments need advanced training to leverage these technologies effectively.

To address this need, the Massachusetts Department of Public Health (MADPH), Harvard Medical School (HMS), the Broad Institute of MIT and Harvard, and the Massachusetts Consortium on Pathogen Readiness (MassCPR) were named as the Lead Pathogen Genomics Center of Excellence (PGCoE) for Education. This initiative, part of the Centers for Disease Control and Prevention (CDC)-funded PGCoE network, provides state-of-the-art training and resources to prepare the public health workforce for pathogen genomic surveillance and outbreak response.

Core Aims

The Lead PGCoE for Education has three core aims

  1. Assess Needs: Perform a landscape analysis to identify gaps in knowledge, training, and workforce capacity, guiding development of educational offerings.
  2. Create a PGCoE Portal and Accreditation Program: Aggregate and adapt existing PGCoE curricula while developing new content for asynchronous and synchronous learning modules.
  3. Develop Advanced Learning Opportunities: Offer additional experiential courses and programs for innovative learning experiences.

PGCoE Education Program

  • Overview

    The PGCoE Education Program offers flexible, self-paced online courses to build knowledge and practical skills in pathogen genomic epidemiology. Developed with support from CDC/OAMD, these courses are designed for professionals in infectious disease preparedness and response, including laboratory scientists, bioinformaticians, and epidemiologists.

  • Why These Courses Exist

    • Developed by the PGCoE Network: Courses are created by the CDC-funded PGCoE network to strengthen national public health workforce competencies in genomic epidemiology.
    • Practice-Informed Curriculum: Content reflects priorities identified by practitioners and supplements existing training and mentoring opportunities.
    • Flexible and Accessible Learning: Courses are free, nationally available, and self-paced. Teams may coordinate participation to enhance shared understanding and collaboration.

  • Featured Courses Available Early 2026

    Foundations I: Conceptual Foundations of Pathogen Genomics 

    • Gain a foundational understanding of pathogen genomics and its value in infectious disease surveillance and response.
    • No prior knowledge of genomics or molecular biology is required.
    • Open to all registrants.

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

    • Explore the molecular mechanisms of genomic sequencing and how data inform public health epidemiology.
    • Open to all registrants; prior genomics knowledge is helpful but not required. Completion of Foundations I is recommended but not mandatory.
    • Learn how pathogens accumulate mutations, generating genomic patterns that reveal transmission dynamics.
    • Introduction to phylogenetics and the analysis of evolutionary relationships using genomic “trees.”
    • Understand how integrating genomic and epidemiologic data—like contact tracing and case demographics—enhances outbreak investigations and decision-making.
    Explore the courses