Gensheimer Kathleen, Allard Marc W, Timme Ruth E, Brown Eric, Hintz Leslie, Pettengill Jamie, Strain Errol, Tallent Sandra M, Vélez Lili F, King Ewa, Shea Sharon L
Author Affiliations: Microbiology, Human Foods Program, US Food and Drug Administration, College Park, Maryland (Gensheimer, Allard, Timme, Brown, Hintz, Pettengill, Strain, Tallent, Vélez); and Association of Public Health Laboratories, Bethesda, Maryland (King, Shea).
J Public Health Manag Pract. 2025;31(3):351-359. doi: 10.1097/PHH.0000000000002090. Epub 2024 Nov 14.
The genomic surveillance of foodborne pathogens in the United States has grown exponentially in the past decade, grounded in a powerful combination of novel sequencing technologies, bioinformatic approaches, data-sharing networks, and metadata harmonization efforts. This practice report examines recent advances in genomic epidemiology as applied to food safety programs and delineates State, Tribal, Local, and Territorial infrastructure necessary for continued life-saving improvements in public health.
National databases of foodborne pathogen genomes, along with data sharing and evaluation networks such as GenomeTrakr and PulseNet, have transformed how connections are made among isolates and how root causes of outbreaks are determined, allowing much more timely interventions to protect public health. Freely available bioinformatics tools such as GalaxyTrakr and the National Center for Biotechnology Information Pathogen Detection database have allowed laboratories with limited local computing resources to participate in surveillance efforts and contribute to traceback investigations.
In this report, we describe advances in genomic epidemiology that have occurred over the past decade and examine obstacles to fully implementing this technology within State, Tribal, Local, and Territorial public health systems.
Despite a clear return on investment from governmental expenditures on genomic surveillance of foodborne pathogens, we identify significant obstacles to further sustained progress. These obstacles include workforce gaps, ineffective data sharing, and lack of constitutive and sustained funding.
Many public health laboratories face major obstacles to widespread and routine adoption of genomic surveillance technologies. While whole genome sequencing has become an integral part of routine public health microbiology, the seamless integration of these protocols into the existing practices, laboratory workflows, and information systems remains challenging. Centralized efforts to address these issues include (1) support through the Food and Drug Administration Laboratory Flexible Funding Model, (2) training and proficiency assessments, (3) open-source, standardized protocols for collecting high-quality genomic data, and (4) open access informatics software.
在过去十年中，美国食源性病原体的基因组监测呈指数级增长，这得益于新型测序技术、生物信息学方法、数据共享网络和元数据协调工作的有力结合。本实践报告探讨了应用于食品安全计划的基因组流行病学的最新进展，并描述了州、部落、地方和领地层面为持续改善公共卫生状况以挽救生命所必需的基础设施。
食源性病原体基因组的国家数据库，以及诸如GenomeTrakr和PulseNet等数据共享与评估网络，已经改变了分离株之间的关联方式以及疫情爆发根源的确定方式，从而能够进行更及时的干预以保护公众健康。诸如GalaxyTrakr和美国国立生物技术信息中心病原体检测数据库等免费生物信息学工具，使当地计算资源有限的实验室能够参与监测工作并为溯源调查做出贡献。
在本报告中，我们描述了过去十年中基因组流行病学取得的进展，并审视了在州、部落、地方和领地公共卫生系统中全面实施这项技术所面临的障碍。
尽管政府在食源性病原体基因组监测方面的支出有明显的投资回报，但我们发现进一步持续取得进展存在重大障碍。这些障碍包括劳动力缺口、数据共享效率低下以及缺乏固定和持续的资金。
许多公共卫生实验室在广泛且常规采用基因组监测技术方面面临重大障碍。虽然全基因组测序已成为常规公共卫生微生物学的一个组成部分，但将这些方案无缝整合到现有实践、实验室工作流程和信息系统中仍然具有挑战性。解决这些问题的集中努力包括：（1）通过食品药品监督管理局实验室灵活资助模式提供支持；（2）培训和能力评估；（3）用于收集高质量基因组数据的开源标准化方案；（4）开放获取的信息学软件。
