Proceedings of a Workshop

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This activity was supported by a contract between the National Academy of Sciences and American Society of Tropical Medicine and Hygiene, Burroughs Wellcome Fund (Contract No. 1195124), Centers for Disease Control and Prevention (Contract No. 75D30121D11240, Order No. 75D30122F00011), EcoHealth Alliance, Infectious Diseases Society of America, Johnson & Johnson (Contract No. C2023026615), Merck and Co., Inc. (Grant No. MEM-22-160471), National Institute of Allergy and Infectious Diseases, National Institutes of Health (Contract No. HHSN263201800029I, Task Order No. 75N98023F00023), New Venture Fund (Contract No. NVF-NGDF-NAT10-Subgrant-022263-2023-08-01), Society of Infectious Diseases Pharmacists, U.S. Agency for International Development (Contract No. 7200AA18GR00003), Uniformed Services University of the Health Sciences (Contract No. HU00012210001), and U.S. Department of Veterans Affairs (Contract No. 36C25024P0225).

Any opinions, findings, conclusions, or recommendations expressed in this publication do not necessarily reflect the views of any organization or agency that provided support for the project.

International Standard Book Number-13: 978-0-309-09984-4
International Standard Book Number-10: 0-309-09984-6
Digital Object Identifier: https://doi.org/10.17226/29103

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Suggested citation: National Academies of Sciences, Engineering, and Medicine. 2025. Accelerating the use of pathogen genomics and metagenomics in public health: Proceedings of a workshop. Washington, DC: National Academies Press. https://doi.org/10.17226/29103.

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PLANNING COMMITTEE ON ACCELERATING THE USE OF PATHOGEN GENOMICS AND METAGENOMICS IN PUBLIC HEALTH¹

DAVID BLAZES (Chair), Gates Foundation

GREGORY ARMSTRONG, Ridgway Consulting, LLC

ANA BENTO, Cornell University College of Veterinary Medicine

CHRISTOPHER BRADEN, National Center for Emerging Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention

RICK BRIGHT, Bright Global Health

LILIANA BROWN, National Institute of Allergy and Infectious Diseases, National Institutes of Health

WONDWOSSEN GEBREYES, Global One Health Initiative, The Ohio State University

SAM HALABI, Georgetown University School of Health

LARRY MADOFF, Massachusetts Department of Public Health

AMEET PINTO, Georgia Institute of Technology

JILL TAYLOR, Association of Public Health Laboratories

Staff

ELIZABETH ASHBY GUO, Program Officer

CLAIRE BIFFL, Research Associate (through July 2024)

TAYLOR WINDMILLER, Senior Program Assistant (from January 2024)

JULIE LIAO, Director, Forum on Microbial Threats

JULIE PAVLIN, Science Advisor, Health and Medicine Division; Senior Board Director, Board on Global Health

___________________

¹The National Academies of Sciences, Engineering, and Medicine’s planning committees are solely responsible for organizing the workshop, identifying topics, and choosing speakers. The responsibility for the published Proceedings of a Workshop rests with the workshop rapporteurs and the institution.

FORUM ON MICROBIAL THREATS¹

PETER DASZAK (Chair), EcoHealth Alliance

CRISTINA CASSETTI (Vice Chair), National Institute of Allergy and Infectious Diseases, National Institutes of Health

KENT E. KESTER (Vice Chair), Coalition for Epidemic Preparedness Innovations

EMILY ABRAHAM, Johnson & Johnson

KEVIN ANDERSON, retired, U.S. Department of Homeland Security

DAN H. BAROUCH, Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center

DANIEL BAUSCH, National University of Singapore

NAHID BHADELIA, Boston University Center for Emerging Infectious Disease

CHRISTOPHER BRADEN, National Center for Emerging Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention

RICK A. BRIGHT, Bright Global Health

AMBIKA BUMB, Bipartisan Commission on Biodefense

ANDREW CLEMENTS, Emerging Threats Division, U.S. Agency for International Development

TRACEY DUTCHER, U.S. Department of Homeland Security

GREG FRANK, Merck & Co., Inc.

WONDWOSSEN GEBREYES, Global One Health Initiative, The Ohio State University

BRUCE G. GELLIN, Georgetown University School of Medicine

GIGI KWIK GRONVALL, Johns Hopkins University Center for Health Security

ELIZABETH D. HERMSEN, Pfizer

KEITH P. KLUGMAN, Gates Foundation

ALBERT I. KO, Yale School of Public Health

LINDA S. LLOYD, San Diego State University School of Public Health

SYRA MADAD, NYC Health + Hospitals

VICTORIA MCGOVERN, Burroughs Wellcome Fund

SUMIKO MEKARU, The Public Health Company

TIMOTHY D. MURRAY, Washington State University

MELISSA NOLAN, University of South Carolina

RAFAEL OBREGÓN, UNICEF

BENJAMIN PINSKY, Stanford University School of Medicine

AMEET J. PINTO, Georgia Institute of Technology

___________________

¹The National Academies of Sciences, Engineering, and Medicine’s forums and roundtables do not issue, review, or approve individual documents. The responsibility for the published Proceedings of a Workshop rests with the workshop rapporteurs and the institution.

P. DAVID ROGERS, St. Jude Children’s Research Hospital

GARY A. ROSELLE, Veterans Health Administration, U.S. Department of Veterans Affairs

UMAIR SHAH, Washington State Department of Health

JONATHAN SLEEMAN, U.S. Geological Survey Wildlife Health Center

MATTHEW ZAHN, Orange County Health Care Agency (California)

Forum on Microbial Threats Staff

ELIZABETH ASHBY GUO, Program Officer

CLAIRE BIFFL, Research Associate (through July 2024)

TAYLOR WINDMILLER, Senior Program Assistant (from January 2024)

JULIE LIAO, Director, Forum on Microbial Threats

JULIE PAVLIN, Science Advisor, Health and Medicine Division (through March 2025)

Reviewers

This Proceedings of a Workshop was reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise. The purpose of this independent review is to provide candid and critical comments that will assist the National Academies of Sciences, Engineering, and Medicine in making each published proceedings as sound as possible and to ensure that it meets the institutional standards for quality, objectivity, evidence, and responsiveness to the charge. The review comments and draft manuscript remain confidential to protect the integrity of the process.

We thank the following individuals for their review of this proceedings:

Although the reviewers listed above provided many constructive comments and suggestions, they were not asked to endorse the content of the proceedings nor did they see the final draft before its release. The review of this proceedings was overseen by ANN M. ARVIN, Stanford University. She was responsible for making certain that an independent examination of this proceedings was carried out in accordance with standards of the National Academies and that all review comments were carefully considered. Responsibility for the final content rests entirely with the rapporteurs and the National Academies.

Contents

ACRONYMS AND ABBREVIATIONS

1 INTRODUCTION

Workshop Objectives

Organization of the Proceedings of the Workshop

2 EXPLORING THE CURRENT STATE OF PATHOGEN GENOMICS AND METAGENOMICS IN THE U.S. PUBLIC HEALTH ENTERPRISE

Current Status of Pathogen Genomics in U.S. Public Health

Applications of Pathogen Genomics in Public Health: National Level

Applications of Pathogen Genomics in Public Health: State Level

Discussion

3 APPLICATIONS IN EARLY WARNING AND PREPAREDNESS

Genomics to Address Antimicrobial Resistance

Wastewater Tracking of Pathogen Dynamics

Genomic Sequencing to Inform Therapeutic Usage

Pathogen Genomics for Outbreak Epidemiology

Applications of Pathogen Genomics in H5N1 Dairy Cattle Outbreak

Discussion

4 DATA INFRASTRUCTURE, INTEROPERABILITY, CLASSIFICATION, AND STEWARDSHIP

Exploring the Current State of Infrastructure and Interoperability of Pathogen Genomics Data in the United States

Integration of Data Streams to Augment Genomic Data

PHA4GE: Bridging the Gap Between Public Health and Bioinformatics

Data Processing Structures and Determining the Value of Sequenced Data

Discussion

5 PRIVACY, OWNERSHIP, AND ACCESSIBILITY CONSIDERATIONS IN THE UNITED STATES

International Governance of Pathogen Genomics Data

Privacy and Ethical Considerations Related to Human Genome Sequences in Public Health Datasets

Ethical Issues in Pathogen Genomics

Democratization Efforts and Integration of Alternate Data Systems

Discussion

6 GAPS AND OPPORTUNITIES IN APPLICATIONS, FUNDING, AND RESEARCH

Applications for New Pathogen Detection and Limitations of Genomics Data

Strengthening the Applied Genomic Epidemiology Workforce

Gaps and Opportunities for Public Health Investments in Enteric Diseases

Discussion

7 ENVISIONING THE FUTURE OF PATHOGEN GENOMICS

Accelerating the Use of Pathogen Genomics and Metagenomics in Public Health

Exploring the Potential of Pathogen Genomics

Discussion

8 FINAL THOUGHTS

Day 1 Synthesis

Day 2 Synthesis

REFERENCES

APPENDIXES

A Workshop Statement of Task

B Public Meeting Agenda

Box and Figures

BOX

5-1 Case Study: Privacy Implications in Wastewater Surveillance

FIGURES

3-1 Aiming for impact with work on genomics in antimicrobial resistance

4-1 INSDC-compliant Pathogen Data Object Model to structure genomic data for public health applications

7-1 Dimensions of collaborative surveillance

Acronyms and Abbreviations