Abstract：
Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. Streptococcus pneumoniae (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries, including Israel. To understand the geographical spread of the pneumococcus in Israel, we analysed 1174 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole-genome data within a relative risk (RR) ratio framework to capture the geographical structure of S. pneumoniae. While we could not find geographical structure at the overall lineage level, the extra granularity provided by whole-genome sequence data showed that it takes approximately 5 years for invasive pneumococcal isolates to become fully mixed across the country.This article contains data hosted by Microreact.
摘要：
了解病原体如何在地理空间中传播是疫苗接种等控制措施的基础。肺炎链球菌（肺炎球菌）是一种呼吸道细菌，占全球传染病发病率和死亡率的很大一部分。即使在疫苗接种后的时代，侵袭性肺炎球菌病（IPD）的发病率在大多数国家保持稳定，包括以色列。为了了解肺炎球菌在以色列的地理分布，我们分析了来自多个区域的IPD患者的1174个肺炎球菌基因组.我们将使用全基因组数据推断的分离株对之间的进化距离纳入相对风险（RR）比率框架，以捕获肺炎链球菌的地理结构。虽然我们在整个血统层面上找不到地理结构，全基因组序列数据提供的额外粒度表明,侵袭性肺炎球菌分离株在全国范围内完全混合大约需要5年.本文包含Microreact托管的数据。
