Increasingly, public-health agencies are using pathogen genomic sequence data to support surveillance and epidemiological investigations. As access to whole-genome sequencing has grown, greater amounts of molecular data have helped improve the ability to detect and track outbreaks of diseases such as COVID-19, investigate transmission chains and explore large-scale population dynamics, such as the spread of antibiotic resistance. However, the wide adoption of whole-genome sequencing also poses new challenges for public-health agencies that must adapt to support a new set of expertise, which means that the capacity to perform genomic data assembly and analysis has not expanded as widely as the adoption of sequencing itself. In this Perspective, we make recommendations for developing an accessible, unified informatic ecosystem to support pathogen genomic analysis in public-health agencies across income settings. We hope that the creation of this ecosystem will allow agencies to effectively and efficiently share data, workflows and analyses and thereby increase the reproducibility, accessibility and auditability of pathogen genomic analysis while also supporting agency autonomy.

公共卫生机构越来越多地使用病原体基因组序列数据来支持监测和流行病学调查。随着全基因组测序的普及，更多的分子数据有助于提高检测和跟踪 COVID-19 等疾病爆发、调查传播链和探索大规模群体动态（例如抗生素传播）的能力反抗。然而，全基因组测序的广泛采用也给公共卫生机构带来了新的挑战，它们必须适应支持一套新的专业知识，这意味着进行基因组数据组装和分析的能力并没有像采用那样广泛扩展。测序本身。在本视角中，我们建议开发一个可访问的、统一的信息生态系统，以支持跨收入环境的公共卫生机构的病原体基因组分析。我们希望这个生态系统的创建将使各机构能够有效和高效地共享数据、工作流程和分析，从而提高病原体基因组分析的可重复性、可访问性和可审计性，同时支持机构自主权。