1. Plague: Out of the Foothills
Rebecca E. Colman1, Robert J. Brinkerhoff2, Adina Doyle1, Chris Ray3, Paul Keim1, Sharon K. Collinge3, and David M. Wagner1
1Northern Arizona University, Flagstaff, AZ; 2Yale University, New Haven, CT; 3University of Colorado at Boulder, Boulder, CO
Study of CO plague over one season and it a collaboration with Sharon Collinge

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

3. Plague in North America
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

4. So what is the reservoir?
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

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

6. Cycle: Enzootic / Epizootic

7. Study System: Boulder Colorado
Sites with Y. pestis positive samples from June to September 2005

8. Study Questions
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?

9. Hypothetical Molecular Trees
Out of the Foothills hypothesis
Other local reservoir hypothesis F A E D B F A E D C B C

10. Collection Methods 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

11. Different Molecular Markers
Fast
Slow
Mutation Rate
10-3
10-4
10-5
10-6
10-7
10-8
10-9
10-10
Complex VNTRs
SNPs
SNR / VNTRs

12. MLVA Multi-Locus Variable number tandem repeat Analysis Insertion
Deletion

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

14. MLVA Results 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

15. MLVA Results

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

17. SNP Results Whole Genome Sequence comparisons
Northern AZ
Colorado
Whole Genome Sequence comparisons
SNPs are extremely rare Y. pestis
Show historical divergence
Samples fell out into two SNP groups

18. SNP and MLVA combined

19. Conclusion
Geographic proximity does not equal genetic similarity

20. Implications
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

21. Implications
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?

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

23. Questions ?