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.
Highlights
Three pandemics caused by Yersinia pestis claimed hundreds of thousands of human lives and reshaped the history of human civilization [1,2]
We used a two-step phylogenetic analysis that is based on different sets of genomes to prove that the 2009 plague outbreak originated from the infection of Y. pestis that circulated in a local region as well as verified the previous conclusion of dog–human transmission [31]
The first step was to define the phylogenetic position of outbreak isolates by comparing the representative strains of Y. pestis with worldwide ones to deduce a preliminary outbreak origin
Summary
Three pandemics caused by Yersinia pestis claimed hundreds of thousands of human lives and reshaped the history of human civilization [1,2]. The major clinical forms of plague are bubonic, pneumonic, and septicemic. The pneumonic plague is the most threatening one because it is transmitted by respiratory droplets from person to person [3]. The natural plague foci of Y. pestis are still widely distributed in Asia, Africa, America, and Eastern Europe, and many new cases are reported to the World Health Organization each year [4]. A major concern about the plague is that Y. pestis strains are acquired from widely distributed natural foci and can be used for bioterrorism. Y. pestis is classified by the U.S Centers for Disease Control and Prevention as a Category A bioterrorism agent [5]
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