PDF(Pubmed)
Abstract：
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 used cholera case-count data. More recently, whole-genome sequence data have 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 to 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.
摘要：
霍乱仍然是全球健康威胁。了解霍乱如何在不同地点之间传播是理性的基础，干预和控制工作的循证设计。传统上,霍乱传播模型使用霍乱病例计数数据。最近,全基因组序列数据定性描述了霍乱传播.整合这些数据流可以提供更准确的霍乱传播模型；然而，到目前为止,尚未对传统病例计数模型与来自基因组数据的霍乱传播系统动力学模型进行系统分析.这里,我们使用阿根廷1991~1998年霍乱疫情的高保真病例计数和全基因组测序数据,直接比较从这两种数据来源估算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既定方法一致的可比估计。我们的方法代表了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关键步骤。
