Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen.
Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen.
复制标题
使用系统动力学推断环境传播：使用肠道病原体模拟进化的案例研究。
DOI：
10.1098/rsif.2021.0041
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Lanzas,Cristina
中科院分区：
文献类型：
--
作者：
Dawson,Daniel;Rasmussen,David;Peng,Xinxia;Lanzas,Cristina
Indirect (environmental) and direct (host–host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. In this study, we used a network-based transmission model that explicitly models pathogen evolution to simulate epidemics with both direct and indirect transmission. Epidemics were simulated according to factorial combinations of direct/indirect transmission proportions, host mutation rates and conditions of environmental pathogen growth. Transmission trees were then reconstructed using the phylodynamic approach SCOTTI (structured coalescent transmission tree inference) and evaluated. We found that although insufficient diversity sets a lower bound on when accurate phylodynamic inferences can be made, transmission routes and assumed pathogen lifestyle affected pathogen population structure and subsequently influenced both reconstruction success and the likelihood of direct versus indirect pathways being reconstructed. We conclude that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.
