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Abstract
Plague disease caused by the Gram-negative bacterium Yersinia pestis routinely affects animals and occasionally humans, in the western United States. The strains native to the North American continent are thought to be derived from a single introduction in the late 19th century. The degree to which these isolates have diverged genetically since their introduction is not clear, and new genomic markers to assay the diversity of North American plague are highly desired. To assay genetic diversity of plague isolates within confined geographic areas, draft genome sequences were generated by 454 pyrosequencing from nine environmental and clinical plague isolates. In silico assemblies of Variable Number Tandem Repeat (VNTR) loci were compared to laboratory-generated profiles for seven markers. High-confidence SNPs and small Insertion/Deletions (Indels) were compared to previously sequenced Y. pestis isolates. The resulting panel of mutations allowed clustering of the strains and tracing of the most likely evolutionary trajectory of the plague strains. The sequences also allowed the identification of new putative SNPs that differentiate the 2009 isolates from previously sequenced plague strains and from each other. In addition, new insertion points for the abundant insertion sequences (IS) of Y. pestis are present that allow additional discrimination of strains; several of these new insertions potentially inactivate genes implicated in virulence. These sequences enable whole-genome phylogenetic analysis and allow the unbiased comparison of closely related isolates of a genetically monomorphic pathogen.
Highlights
Yersinia pestis, the etiologic agent of plague disease, exists worldwide in discrete enzootic foci that contain genotypically and often phenotypically distinct variants [1,2]
Yersinia pestis, which arrived in North America during the third global pandemic in the early 20th century, is commonly thought to have entered the Continental United States through the port of San Francisco [23], as some of the earliest reports of enzootic plague originated in that city
A recent phylogenetic analysis suggests a possible route of importation into Southern California [1]
Summary
The etiologic agent of plague disease, exists worldwide in discrete enzootic foci that contain genotypically and often phenotypically distinct variants [1,2]. Some recent reports, including a whole-genome sequence of an isolate from the 14th century pandemic, demonstrate that strains from a more deeply rooted branch of the Y. pestis lineage may have caused the Black Death [7,8]. Because no preexisting plague foci were present on the North American continent, the plague reservoirs (mostly in small rodent populations) contained exclusively this biotype and are thought to have relatively little genetic diversity. The apparent lack of diversity may be the result of discovery bias, as the phylogenetic analyses to date have relied on only three North American plague genome sequences [1,10,11,12]
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