论文标题
局部霍乱暴发模型中基因组和流行病学数据的一致性
Congruity of genomic and epidemiological data in modeling of local cholera outbreaks
论文作者
论文摘要
霍乱仍然是全球健康威胁。了解霍乱如何在位置之间传播是理性的，基于证据的干预和控制工作的基础。传统上，霍乱传播模型利用了霍乱案例计数数据。最近，整个基因组序列数据已定性地描述了霍乱传播。整合这些数据流可能会提供更准确的霍乱差异模型，但是到目前为止，尚未进行系统的分析，以将传统的病例计数模型与从霍乱传播的基因组数据中进行比较的系统动力学模型。在这里，我们使用1991 - 1998年阿根廷霍乱流行的高保真案例计数和整个基因组测序数据直接比较了从这两个数据源估计的流行病学模型参数。我们发现，应用于霍乱基因组学数据的系统动力学方法提供了与已建立方法一致的可比估计值。我们的方法是建立框架以整合霍乱流行病学和其他细菌病原体的病例计数和基因组数据源的框架的关键步骤。
Cholera continues to be a global health threat. Understanding how cholera spreads between locations is fundamental to the rational, evidence-based design of intervention and control efforts. Traditionally, cholera transmission models have utilized cholera case count data. More recently, whole genome sequence data has qualitatively described cholera transmission. Integrating these data streams may provide much more accurate models of cholera spread, however no systematic analyses have been performed so far to compare traditional case-count models to the phylodynamic models from genomic data for cholera transmission. Here, we use high-fidelity case count and whole genome sequencing data from the 1991-1998 cholera epidemic in Argentina to directly compare the epidemiological model parameters estimated from these two data sources. We find that phylodynamic methods applied to cholera genomics data provide comparable estimates that are in line with established methods. Our methodology represents a critical step in building a framework for integrating case-count and genomic data sources for cholera epidemiology and other bacterial pathogens.
