title: Two-step source tracing strategy of Yersinia pestis and its historical epidemiology in a specific region.
abstract: Source tracing of pathogens is critical for the control and prevention of infectious diseases. Genome sequencing by high throughput technologies is currently feasible and popular, leading to the burst of deciphered bacterial genome sequences. Utilizing the flooding genomic data for source tracing of pathogens in outbreaks is promising, and challenging as well. Here, we employed Yersinia pestis genomes from a plague outbreak at Xinghai county of China in 2009 as an example, to develop a simple two-step strategy for rapid source tracing of the outbreak. The first step was to define the phylogenetic position of the outbreak strains in a whole species tree, and the next step was to provide a detailed relationship across the outbreak strains and their suspected relatives. Through this strategy, we observed that the Xinghai plague outbreak was caused by Y. pestis that circulated in the local plague focus, where the majority of historical plague epidemics in the Qinghai-Tibet Plateau may originate from. The analytical strategy developed here will be of great help in fighting against the outbreaks of emerging infectious diseases, by pinpointing the source of pathogens rapidly with genomic epidemiological data and microbial forensics information.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China ; BGI-Shenzhen, Shenzhen, China.
authors.forename: Yanfeng
authors.initials: Y
authors.lastname: Yan
authors.affiliation: Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China.
authors.forename: Hu
authors.initials: H
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Dongfang
authors.initials: D
authors.lastname: Li
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Xianwei
authors.initials: X
authors.lastname: Yang
authors.affiliation: Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China.
authors.forename: Zuyun
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China.
authors.forename: Zhizhen
authors.initials: Z
authors.lastname: Qi
authors.affiliation: Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China.
authors.forename: Qingwen
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China.
authors.forename: Baizhong
authors.initials: B
authors.lastname: Cui
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Zhaobiao
authors.initials: Z
authors.lastname: Guo
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Chang
authors.initials: C
authors.lastname: Yu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Computer Science, National University of Defense Technology, Changsha, China.
authors.forename: Guangming
authors.initials: G
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Yajun
authors.initials: Y
authors.lastname: Song
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China ; BGI-Shenzhen, Shenzhen, China.
authors.forename: Yujun
authors.initials: Y
authors.lastname: Cui
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China ; BGI-Shenzhen, Shenzhen, China.
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
mesh_terms: D000818:Animals; D004196:Disease Outbreaks; D004285:Dogs; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D010802:Phylogeny; D010930:Plague / Q000453:epidemiology* / Q000382:microbiology / Q000635:transmission; D012589:Sciuridae / Q000382:microbiology; D017422:Sequence Analysis, DNA; D005423:Siphonaptera / Q000382:microbiology; D018609:Tibet / Q000453:epidemiology; D015010:Yersinia pestis / Q000145:classification / Q000235:genetics*