Sintchenko Vitali, Sim Eby M, Suster Carl J E
School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.
Sydney Infectious Diseases Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.
Sci Data. 2025 May 13;12(1):784. doi: 10.1038/s41597-025-05049-x.
The COVID-19 pandemic has illuminated the utility of pathogen genomics and highlighted roadblocks to international data sharing. This article describes the deferred value of pathogen genomics data for secondary use using a set of 10,110 assembled genomes of Vibrio cholerae shared via international repositories between 2010 and 2024 as an illustrative representation of a pandemic disease. Trends in the quality, representativeness, and timeliness of data sharing as well as the increasing role of microbiology services as genomic data providers resulting from gradually improving access to sequencing technologies in countries with a high burden of disease were identified. The deferred value of individual and aggregated genomic data was tracked over time and mapped to geographical hot spots of cholera. The time lag between the collection of the samples for V. cholerae cultures and the submission of the genome to an international database remained eight years on average. The data value assessment described here paves the way for the international mobilization of quality microbial genomic data for global health and knowledge discovery.
新冠疫情凸显了病原体基因组学的作用，也突显了国际数据共享的障碍。本文以2010年至2024年间通过国际储存库共享的一组10110个霍乱弧菌组装基因组为例，描述了病原体基因组学数据用于二次利用的潜在价值。研究确定了数据共享在质量、代表性和及时性方面的趋势，以及随着疾病负担较重国家测序技术获取途径的逐渐改善，微生物学服务作为基因组数据提供者的作用日益增强。随着时间的推移，对个体和汇总基因组数据的潜在价值进行了跟踪，并绘制到霍乱的地理热点地区。霍乱弧菌培养样本采集与基因组提交至国际数据库之间的时间间隔平均仍为八年。本文所述的数据价值评估为全球健康和知识发现的优质微生物基因组数据的国际动员铺平了道路。
