Two articles have come to my attention over the couple months that argue strongly for an environmental role in plague epidemics/epizootics over clonal expansion. Taken together these studies suggest that multiple strains of Yersinia pestis percolate out of multiple reservoirs at the same time.
The strongest support comes from Madagascar where ten MLVA defined strains from 93 human clinical specimens representing the two major groups of Yersinia pestis (based on, if I recall correctly, their introduction source) all emerged within one single year, 2007, scattered over a large range of the central island. These ten strains represent eight previously known strains and two discovered in this investigation. As the map shows, several locations had cases from more than one lineage. This pattern does not suggest to me that one strain was more successful than another; there is no new mutation that allowed one strain to erupt on the scene or transmission advantage caused by chance or mutation. (Yes, chance does play a role sometimes.) That one strain is more widespread than another probably represents years of enzootic spread and so multiple emergences of a more common strain. With multiple strains emerging at the same time, there is relatively little clonal or territorial expansion, and no reason to expect a major selective advantage by any particular strain. They are emerging where ever the right environmental conditions exist. This study is not directly informative on the underlying epizootic. There may have been even more strain diversity in the epizootic.
There are at least two relevant findings for future surveillance. First, these strains were genotyped directed from DNA in clinical specimens without culturing the specimen. This means that specimens that previously were difficult to culture can still be genotyped and it also should be safer for lab staff to handle. It suggests again that they need a new case classification system since only culturable isolates are considered confirmed. As encouraging as this is, the bad news for reservoir surveillance is that they will have to monitor very large zones based on climate and other environmental factors instead of just trying to project the direction of an ongoing outbreak.
This is supported by another study published in May by Jennifer Lowell’s team on plague in the western US. They analyzed 34 isolates of Yersinia pestis collected from fleas, humans, cats, and a variety of other animals between 1980 and 2006 primarily in Colorado (21) and some scattered sites across the southwest. In Colorado isolates geographically close but temporally spaced showed an evolutionary relationship demonstrating that they had evolved in place over seven years. Mountain isolates were also distinctive between valleys and on the plains suggesting that they evolved in isolation.
During the initial introduction of Yersinia pestis to a region, there is a rapid spread of a single clone but following this, there the creation of local reservoirs with evolution occurring in place. Subsequent epizootics emerge from these new reservoirs and remain small. It follows that large epizootics are usually the emergence of several reservoirs stimulated by the right environmental conditions.
What I take from this is the idea that large scale spread of epizootics or epidemics over different ecological regions require human assistance. There is a anthropogenic factor to the largest epizootics/epidemics. Left to their own means, epizootics remain local spreading only as far as the contiguous environment allows. Some agent, usually humans, must carry them between permissive environments. It is possible that the permissive environment will be urban as it was in Madagascar in the 1990s (Vogler et al, 2013).
Now thinking historically, what we need is serial aDNA results from the same city over many centuries. London and Marseille would be good options, so would Constantinople and Alexandria. With enough aDNA samples it should be possible to estimate how many introductions of Yersinia pestis from the Asia occurred for each pandemic and to discern a role for European or Mediterranean local reservoirs. These modern studies are absolutely necessary to make sense out of the patterns that will eventually emerge when we have enough aDNA specimens.
Riehm, J. M., Projahn, M., Vogler, A. J., Rajerison, M., Andersen, G., Hall, C. M., et al. (2015). Diverse Genotypes of Yersinia pestis Caused Plague in Madagascar in 2007. PLoS Neglected Tropical Diseases, 9(6), e0003844. doi:10.1371/journal.pntd.0003844.s002 (h/t to Matt Wilson for this one!)
Lowell, J. L., Antolin, M. F., Andersen, G. L., Hu, P., Stokowski, R. P., & Gage, K. L. (2015). Single-Nucleotide Polymorphisms Reveal Spatial Diversity Among Clones of Yersinia pestis During Plague Outbreaks in Colorado and the Western United States. Vector Borne and Zoonotic Diseases (Larchmont, N.Y.), 15(5), 291–302. doi:10.1089/vbz.2014.1714
Vogler, A., Chan, F., Nottingham, R., Andersen, G., Drees, K., Beckstrom-Sternberg, S., Wagner, D., Chanteau, S., & Keim, P. (2013). A Decade of Plague in Mahajanga, Madagascar: Insights into the Global Maritime Spread of Pandemic Plague mBio, 4 (1) DOI: 10.1128/mBio.00623-12