8

Final Thoughts

DAY 1 SYNTHESIS

Christopher Braden and Sam Halabi, professor at Georgetown University School of Health, provided an overview of the first day of the workshop. Braden noted that technologies for next-generation sequencing (NGS) and computation analyses have advanced as costs have decreased, enabling more effective public health applications. Foodborne disease and tuberculosis programs were among the first U.S. public health applications of NGS; more recent applications include tracking antimicrobial resistance (AMR) and highly pathogenic avian influenza A. All U.S. states now have sequencing technologies for public health in place, and although the high expense and complexity of metagenomics continue to pose challenges, the field holds much promise, said Braden. Researchers are using pathogen genomics to develop wastewater surveillance capability and create the next generation of medical countermeasures. Continued progress in genomic data integration will enable more effective public health applications, noted Braden, adding that numerous data platforms currently offer varied analyses and methods with duplication of effort. Pathogen genomics requires contributions from and communications between diverse disciplines, underscoring the need for next-generation workforce development. Braden remarked on robust collaboration during the COVID-19 pandemic to establish large databases and share information among groups; however, maintaining this level of collaboration remains a challenge as the field moves forward.

Halabi highlighted the tensions that arise when a field like pathogen genomics is expanding from the bottom up but also requires ethical and

legal processes to be institutionalized and codified. He remarked that much work remains to ensure that formal legal and ethical reviews do not constrain progress while also mitigating ethical concerns, pointing to Public Health Alliance for Genomic Epidemiology (PHA4GE) as an example of a community that has created much-needed data-sharing structures. Furthermore, developing the pathogen genomics workforce and meeting diverse workforce needs will require training that extends beyond formal education in highly technical areas, said Halabi. Increased pathogen genomics efforts at county, state, and national levels entail greater outreach, community engagement, and collaboration. Given that only approximately half of the generated sequence data are publicly available, Halabi highlighted the need for incentives to further promote data sharing.

David Blazes provided opening remarks on the second day of the workshop. Blazes reviewed concepts that emerged during the first four sessions, including the value of awareness in facilitating cross-discipline and multisector engagement that overcomes the constraints of organizational silos. He noted that the workshop featured a range of multidisciplinary insights related to pathogen genomics that participants can incorporate into their work. Additionally, the workshop highlighted the breadth of use cases throughout the decades-long evolution of pathogen genomics, underscoring enormous opportunity to incorporate pathogen genomics into public health, said Blazes. Leveraging bioinformatics and developing complementary use cases and multiplex assays would bolster sustainable pathogen genomics systems, he added. Blazes asserted that the achievement of developing a COVID-19 vaccine within a year exemplifies the potential for innovation in product development. Speakers raised data-sharing considerations throughout the workshop and suggested that upstream data governance policies could improve data-sharing practices. Blazes cautioned that the trend toward datasets curated by artificial intelligence (AI) could limit access to data, suggesting that data governance might address the role of AI in data access. Finally, Blazes outlined a vision where integrated disease surveillance systems that incorporate genomics and various data streams could improve public health decision making.

DAY 2 SYNTHESIS

Greg Armstrong remarked that a vision of the day-to-day use of genomic data to improve health dates back to the founding of National Center for Biotechnology Information (NCBI) in 1988 under David Lip-man, and now, in 2024, that vision is being realized as genomics becomes a core component of public health infectious disease surveillance and investigation efforts. He described genomic sequencing as one of the most important laboratory technologies to arise in public health since the invention of

polymerase chain reaction (PCR). The issues surrounding genomic sequencing are complex and include ethical considerations that require additional attention, said Armstrong. He commented that although public health data have always contributed to medical product development, pathogen sequencing has increased this dynamic to an unprecedented level, particularly around development of vaccines and diagnostics. The development of pathogen sequencing technologies with clinical applications will likely create a data flow from clinical medicine back to public health, Armstrong added.

Noting a long-standing divide between the Centers for Disease Control and Prevention’s (CDC’s) laboratory and epidemiology divisions, Armstrong emphasized that pathogen genomics requires the collaboration of molecular genomics experts, bioinformaticians, and epidemiologists with multidisciplinary skills. Workforce needs include the ability to expand focus beyond a specific pathogen or discipline to take a systematic view. Public health workforce development and government networking efforts could yield numerous benefits in advancing the collaborative, multidisciplinary field of pathogen genomics, he remarked. This collaboration should extend to data sharing to capitalize on the potential value of secondary data use. The establishment of data governance policies could support the generation and availability of standardized, interoperable data and address issues including data sovereignty, confidentiality, and appropriate attribution to data sources. Armstrong stated that federated human genomics data initiatives, like the National COVID Cohort Collaborative, demonstrate the benefits of such an approach and offer lessons for the field of pathogen genomics.

Armstrong highlighted areas related to pathogen genomics requiring deeper exploration. Consistent, adequate funding for public health—including pathogen genomics—is needed to disrupt the panic-neglect cycle and establish technology and workforce infrastructure that enable prevention efforts, he maintained. Noting that regulation can support or curtail public health efforts, he remarked that regulation has the potential to stimulate improved accuracy and reliability of diagnostics, but over-regulation stifles innovation. Moreover, laws may conflict with ethical priorities, placing public health workers in situations where they have to contend with the legal obligation to withhold genomic information (e.g., a variant from patients with COVID-19) and the ethical consideration of patient autonomy that allows individuals to decide what health information is important to them. Thus, pathogen genomics in public health entails complex issues requiring balance and further consideration, Armstrong said.

This page intentionally left blank.