Determination of Yersinia pestis population structure as a model for low prevalence/epizootic disease dynamics

The plague is a highly virulent zoonotic disease caused by the gram-negative bacterium Yersinia pestis. This bacterium was introduced in the U.S. in the early 1900s, and has established in rodents of the west and southwest. Occasionally, Y. pestis spills over into humans causing severe and often fatal disease. Determining the spatial arrangement of disease foci will increase our understanding of disease dynamics. The objectives of this study focused on utilizing Y. pestis molecular diversity to identify epizootic sources of human plague infections, and to determine the arrangement of epizootic plague foci in the southwestern U.S. and in Kazakhstan, the hypothesized origin of Y. pestis. Samples were chosen representing three geographic scales, and were analyzed to identify isolates from the same epizootic source. The three geographic scales represented a close scale, an intermediate scale, and a distant scale. We used variable number of tandem repeats (VNTRs) and multi locus variable number of tandem repeat analysis (MLVA) to compare these isolates. The close geographic scale analysis consisted of Y. pestis isolates from infected humans and environmental sources like fleas and rodents collected during corresponding epidemiological investigations. Isolates from distinct clusters of human plague cases in New Mexico, and isolates collected from predefined foci in Kazakhstan were used to analyze Y. pestis population structure on intermediate scales. Isolates from the three Y. pestis biovars from the U.S. and Kazakhstan, were compared for distant geographic scale analyses. While MLVA was useful for inferring Y. pestis isolate relationships on small and large geographic scales, it was not useful for determining population structure of epizootic foci on intermediate scales.; We also identified single nucleotide polymorphisms (SNPs) in the Y. pestis genome using DNA microarrays. We chose isolates from two port cities in California and fifteen Colorado isolates from pre-defined plague foci in the mountains and the PNG to determine population structure among the three areas. Sixty-nine SNPs identified separate Y. pestis populations on the eastern and the western PNG. Isolates from the mountains and one isolate from the eastern plains were similar but weakly supported in phylogenetic analyses.