Genetic diversity and spatial-temporal distribution of Yersinia pestis in Qinghai Plateau, China.

Xiaoyan Yang,Haisheng Wu,Jian He,Yong Jin,Juan Jin,Stephen W Attwood,Xiang Li,Yujun Cui,Qingwen Zhang,Xiaoqing Xu,Zhizhen Qi,Xing Jin,Cunxiang Li,Youquan Xin,Haihong Zhao

doi:10.1371/journal.pntd.0006579

Abstract

BackgroundPlague, caused by the bacterium Yersinia pestis, is a highly infectious, zoonotic disease. Hundreds of human plague cases are reported across the world annually. Qinghai Plateau is one of the most severely affected plague regions in China, with more than 240 fatal cases of Y. pestis in the last 60 years. Conventional epidemiologic analysis has effectively guided the prevention and control of local plague transmission; however, molecular genetic analysis is more effective for investigating population diversity and transmission. In this report, we employed different genetic markers to analyze the population structure of Y. pestis in Qinghai Plateau.Methodology/Principal findingWe employed a two-step hierarchical strategy to analyze the phylogeny of 102 Qinghai Plateau isolates of Y. pestis, collected between 1954 and 2011. First, we defined the genealogy of Y. pestis by constructed minimum spanning tree based on 25 key SNPs. Seven groups were identified, with group 1.IN2 being identified as the dominant population. Second, two methods, MLVA and CRISPR, were applied to examine the phylogenetic detail of group 1.IN2, which was further divided into three subgroups. Subgroups of 1.IN2 revealed a clear geographic cluster, possibly associated with interaction between bacteriophage and Y. pestis. More recently, Y. pestis populations appear to have shifted from the east toward the center and west of Qinghai Plateau. This shift could be related to destruction of the local niche of the original plague focus through human activities. Additionally, we found that the abundance and relative proportion of 1.IN2 subgroups varied by decade and might be responsible for the fluctuations of plague epidemics in Qinghai Plateau.Conclusion/SignificanceMolecular genotyping methods provided us with detailed information on population diversity and the spatial-temporal distribution of dominant populations of Y. pestis, which will facilitate future surveillance, prevention, and control of plague in Qinghai Plateau.

Highlights

Plague, caused by the virulent bacteria Yersinia pestis, is a highly infectious zoonotic disease [1, 2]
Since the first strain of Y. pestis was isolated in Qinghai in 1954, confirmed plague cases have occurred nearly every year, and more than 240 people have died from plague over the past 60 years
Our results indicate that 1.IN2 is the dominant group of Y. pestis in Qinghai Plateau, and its three subpopulations revealed clear geographic clustering that might be driven by interaction with bacteriophages

Summary

Introduction

Plague, caused by the virulent bacteria Yersinia pestis, is a highly infectious zoonotic disease [1, 2]. Y. pestis circulates between multiple species of rodent hosts and species of flea vectors, and persists in multiple natural plague foci in Asia, Europe, Africa, and America, causing hundreds of human plague cases annually. It is reported that at least 20 species of mammals and 11 species of fleas could be infected by Y. pestis in Qinghai Plateau [4]. Some of them, such as Marmota himalayana, act as a reservoir, maintaining Y. pestis transmission in the environment. Qinghai Plateau is one of the most severely affected plague regions in China, with more than 240 fatal cases of Y. pestis in the last 60 years. We employed different genetic markers to analyze the population structure of Y. pestis in Qinghai Plateau

Methods

Results

Discussion

Conclusion