全基因组测序在确定进化缓慢且多变的病原体的可能传播配对方面的作用

IF 3 3区 医学 Q2 INFECTIOUS DISEASES
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引用次数: 0

摘要

病原体全基因组测序(WGS)已被用于非常详细地追踪传染病的传播情况,特别是对于像许多 RNA 病毒那样经历快速而稳定进化的病原体。然而,对于其他病原体来说,进化的可预测性较低,这就使得解释这些数据以帮助我们了解其流行病学更具挑战性,而且密集收集的病原体基因组数据的价值也不确定。在此,我们评估了 WGS 在 "谁感染了谁 "的鉴定问题中对此类病原体的实用性。我们研究了宿主(130 头牛、111 只獾)的样本,这些宿主确诊感染了牛结核杆菌(导致牛结核病),据估计其时钟频率慢至每年 0.1-1 次变化。对于宿主之间的每种潜在途径,我们都会计算发生这种传播事件的相对可能性。这一计算参考了流行病学传播模型和宿主生活史数据。通过纳入 WGS 数据,我们大大减少了可能传播途径的数量,而不是仅根据生活史数据来计算。尽管我们对牛海绵状芽孢杆菌的进化存在不确定性,但 WGS 数据仍是流行病学调查的重要辅助工具,特别是对于生活史数据稀少的野生动物物种。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The utility of whole-genome sequencing to identify likely transmission pairs for pathogens with slow and variable evolution

Pathogen whole-genome sequencing (WGS) has been used to track the transmission of infectious diseases in extraordinary detail, especially for pathogens that undergo fast and steady evolution, as is the case with many RNA viruses. However, for other pathogens evolution is less predictable, making interpretation of these data to inform our understanding of their epidemiology more challenging and the value of densely collected pathogen genome data uncertain. Here, we assess the utility of WGS for one such pathogen, in the “who-infected-whom” identification problem. We study samples from hosts (130 cattle, 111 badgers) with confirmed infection of M. bovis (causing bovine Tuberculosis), which has an estimated clock rate as slow as 0.1–1 variations per year. For each potential pathway between hosts, we calculate the relative likelihood that such a transmission event occurred. This is informed by an epidemiological model of transmission, and host life history data. By including WGS data, we shrink the number of plausible pathways significantly, relative to those deemed likely on the basis of life history data alone. Despite our uncertainty relating to the evolution of M. bovis, the WGS data are therefore a valuable adjunct to epidemiological investigations, especially for wildlife species whose life history data are sparse.

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来源期刊
Epidemics
Epidemics INFECTIOUS DISEASES-
CiteScore
6.00
自引率
7.90%
发文量
92
审稿时长
140 days
期刊介绍: Epidemics publishes papers on infectious disease dynamics in the broadest sense. Its scope covers both within-host dynamics of infectious agents and dynamics at the population level, particularly the interaction between the two. Areas of emphasis include: spread, transmission, persistence, implications and population dynamics of infectious diseases; population and public health as well as policy aspects of control and prevention; dynamics at the individual level; interaction with the environment, ecology and evolution of infectious diseases, as well as population genetics of infectious agents.
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