Rebecca E. Colman 1, Robert J. Brinkerhoff 2, Adina Doyle 1, Chris Ray 3, Paul Keim 1, Sharon K. Collinge 3, and David M. Wagner 1 1 Northern Arizona University, Flagstaff, AZ; 2 Yale University, New Haven, CT; 3 University of Colorado at Boulder, Boulder, CO

 Caused by the bacterium Yersinia pestis Obligate pathogen  Cycles between rodents and their associated fleas  Endemic in several foci around the world

 Entered ~ 1900 at a California shipping port San Francisco area, maybe L.A.  Characterized by large die-offs in rodent populations Increased human risk  Mechanism for maintenance unknown Several theories but how it is sustained in North America is not clear

 NSF-NIH: Landscape Effects on Disease Dynamics in Prairie Dogs; ; University of Colorado; $1,832,715  NSF-NIH: Ecological Drivers of Rodent-borne Disease Outbreaks: Trophic Cascades and Dispersal Waves; ; University of New Mexico; $1,746,268  NSF-NIH: Plague As a Model for Low Prevalence/ epizootic Disease Dynamics; ; Colorado State University; $1,281,000  TOTAL = $4.8 million  NSF-NIH: Landscape Effects on Disease Dynamics in Prairie Dogs; ; University of Colorado; $1,832,715  NSF-NIH: Ecological Drivers of Rodent-borne Disease Outbreaks: Trophic Cascades and Dispersal Waves; ; University of New Mexico; $1,746,268  NSF-NIH: Plague As a Model for Low Prevalence/ epizootic Disease Dynamics; ; Colorado State University; $1,281,000  TOTAL = $4.8 million

 Was introduced into the US ~1900 and rapidly spread to the current distribution  Has become endemic in the Southwest Cully and Williams 2001

(Enzootic)(Epizootic)

Colorado Sites with Y. pestis positive samples from June to September 2005

 Does plague come out of the Foothills “reservoir” hosts and infect the prairie dogs in the grasslands?  Or is there another local reservoir that spills over into the prairie dog colonies?

F A E D B C F A E D C B Out of the Foothills hypothesis Other local reservoir hypothesis

 Rodents were trapped and combed for fleas  DNA from individual fleas was extracted  Extractions were screened with 2 PCR targets Plasmid target (pla) and chromosome target  78 samples were used for high resolution genetic analysis  150 samples were used for more ancestral genetic structure

SNR / VNTRs Complex VNTRs SNPs Mutation Rate FastSlow

 Multi-Locus Variable number tandem repeat Analysis Insertion Deletion

 Examines 43 regions of Y. pestis genome with varying mutation rates  Provide discrimination even among local outbreak samples

 Shows population structure by site  Interesting 5A dispersal event  Reservoir sites are more genetically similar to each other than to the prairie dog sites except for 5A

 Single Nucleotide Polymorphisms  Slow mutating markers compared to MLVA, therefore they are more stable markers  Show more ancestral (historical) population structure

 Whole Genome Sequence comparisons  SNPs are extremely rare Y. pestis  Show historical divergence  Samples fell out into two SNP groups Northern AZColorado

 Geographic proximity does not equal genetic similarity

 Reservoir sites are distinct from each other based on MLVA Suggests plague is cycling between epizootics with no real gene flow  Two SNP groups seen in one study season Suggests separate maintenance and dispersal of this disease on small spatial scale

 SNP group 2.2 (blue) – plague comes out of reservoirs (in the foothills) and infects prairie dog colonies (5A)  However the other 2 prairie dog sites (MK and CR) are distinct and must have come from another introduction event Maybe out of the grassland habitat?

 A collaboration with Sharon Collinge’s group at UC Boulder  Work supported by NIH grant #1R15- AI