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Introduction

Pathogen genomics and metagenomics have enhanced disease surveillance and response efforts by improving the detection and classification of pathogens and outbreaks. The advancement of high-throughput genome sequencing technologies, coupled with decreases in associated costs, has enabled applications of whole genome sequencing and next-generation sequencing¹ to powerful data-driven disease surveillance approaches. Public health use cases demonstrate the effects of such approaches on the speed and accuracy of outbreak detection and on the effectiveness of response efforts. Application of these tools has been critical to characterization of novel emerging pathogens, as well as characterization and response to outbreaks caused by evolving pathogens, from those causing foodborne infections to SARS-CoV-2. The COVID-19 pandemic led to widespread use of genomic sequencing for recognizing and characterizing a novel pathogen and informing response efforts such as the development of diagnostics, therapeutics, and vaccines at unprecedented speed. Opportunities for broader integration and adoption of pathogen genomics and metagenomics in public health could improve the rapidity and effectiveness of infectious disease surveillance and response.

The Forum on Microbial Threats (the forum) of the National Academies of Sciences, Engineering, and Medicine (the National Academies) was established to provide a structured opportunity for stakeholder discussion

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¹ Whole genome sequencing refers to a laboratory procedure that determines all or most of the nucleotides in the genome of a microbe. Next-generation sequencing refers to sequencing technologies that can process a large quantity of genetic material at once (CDC, 2024a).

and scrutiny of critical, and possibly contentious, scientific and policy issues related to research on the prevention, detection, surveillance of, and responses to emerging and reemerging infectious diseases in humans, plants, and animals. The forum generates independent and authoritative discourse to stimulate original thinking about emerging and persistent problems in communicable diseases. Bringing together leaders from government agencies, industry, academia, and nonprofit and philanthropic organizations, the forum’s activities are rooted in the breadth of its expert membership and in the commitment of individual members to participate in and contribute to cross-sector dialogue and collaboration on the most pressing issues across the spectrum of microbial threats.

WORKSHOP OBJECTIVES

On July 22 and 23, 2024, a planning committee under the auspices of the forum organized a public workshop titled Accelerating the Use of Pathogen Genomics and Metagenomics in Public Health.² The aim of the workshop was to explore the use of pathogen genomics and metagenomics data in the U.S. public health system. The workshop featured invited presentations and discussions to consider how next-generation sequencing technology has been applied to surveillance efforts with success and to highlight priority areas for research and investment through examining

• Major gaps in the use of genomics technologies for pathogen surveillance across different levels of the U.S. public health infrastructure, and potential frameworks for integrating metagenomics in this context;
• Approaches to strengthening important support mechanisms, such as computing resources and workforce training, to advance the field of genomic epidemiology (e.g., allowing better analysis and integration of genomic with epidemiological or clinical data);
• Ways to incorporate data stewardship principles to optimize collection and sharing of relevant pathogen (meta)genomic data in the United States (with emphasis on lessons and implications for international coordination), improve the secondary utility of these data generated in public health settings, and inform decisions around data privacy, data sharing, and access to benefits;

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² The planning committee’s role was limited to planning the workshop, and the Proceedings of a Workshop was prepared by the workshop rapporteurs as a factual summary of what occurred at the workshop. Statements, recommendations, and opinions expressed are those of individual presenters and participants and are not necessarily endorsed or verified by the National Academies of Sciences, Engineering, and Medicine, and they should not be construed as reflecting any group consensus.

• Conditions that could enable broader and more coordinated, accelerated, and sustained adoption of these tools and technologies for U.S. public health during outbreak and non-outbreak periods;
• How public health resources could be allocated toward bolstering pathogen genomics surveillance capabilities without detracting from other public health programs and components; and
• Opportunities for multisector partnerships between U.S. and global public health institutions, academia, and the private sector to advance the field in technology innovation and implementation, including the development and sharing of pathogen genomics surveillance resources and capabilities.³

ORGANIZATION OF THE PROCEEDINGS OF THE WORKSHOP

In accordance with the policies of the National Academies, the workshop did not attempt to establish any conclusions or recommendations about needs and future directions, focusing instead on information presented, questions raised, and improvements suggested by individual workshop participants. Chapter 2 explores the current landscape of pathogen genomics applications in public health at the federal and state levels. Chapter 3 describes the use of pathogen genomics in outbreak preparedness and detection via applications including antimicrobial resistance, wastewater surveillance, countermeasure development, and outbreak detection. Chapter 4 considers current data infrastructure and efforts to improve data collection, interoperability, and stewardship. Chapter 5 examines legal and ethical considerations related to privacy, ownership, access, use, and analysis of pathogen genomics data in public health applications. Chapter 6 highlights opportunities to advance the capability to detect, address, and prevent disease outbreaks through clinical applications of metagenomics technology, workforce development, and addressing gaps in surveillance reporting and capacity. Chapter 7 discusses visionary initiatives and potential future applications of pathogen genomics systems to prevent and mitigate disease outbreaks. Chapter 8 summarizes participants’ final thoughts on the research gaps, future opportunities, and considerations discussed during the workshop.

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³ The full Statement of Task is available in Appendix A. The workshop agenda is provided in Appendix B.

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