Category Archives: epidemiology

Presentations on the Plague from the European Association of Archaeologists, Vilnius, Lithuania, 2016

I just discovered that most of the presentations from the “Plague in Diachronic and Interdisciplinary Perspective” session of the Europan Association of Archaeologists meeting in Vilnius, Lithuania on 2 September 2016 are now on YouTube.  I think I have collected them all here. Enjoy 3 hours of plague talks!

Introduction-Plague in diachronic and Interdisciplinary perspective by Marcel Keller

From Mild to Murderous: How Yersinia pestis Evolved to Cause Pneumonic Plague by Wyndham Lathem (30 min)

Reconstructing ancient pathogens – discovery of Yersinia pestis in Eurasia 5,000 Years Ago by Simon Rasmussen (15 min)

Plague in the eastern Mediterranean region 1200-1000 BC? by Lars Walloe (15 min)

Placing the Plague of Justinian in the Yersinia pestis phylogenetic context by Jennifer Klunk (15 min)

A demographic history of the plague bacillus revealed through ancient Yersinia pestis genomes by Maria Spyrou (15 min)

Analysis of a High-coverage Yersinia pestis Genome from a 6th Century Justinianic Plague Victim by Michal Feldman (15 min)

Early medieval burials of plague victims: examples from Aschheim and Altenerding (Bavaria, Germany) by Doris Gutsmiedl-Schumann (15 min)

Fleas, rats and other stories – The palaeoecology of the Black Death by Eva Panagiotakopulu (15 min)

Plague in Valencia, 546: A Case Study of the Integration of Texts and Archaeology by Henry Gruber (15 min)

Germany and the Black Death: a zooarchaeological approach by M.A. Paxinos

Reservoirs of Salt Adapted Yersinia pestis

The Arab Maghreb is one of the most arid environments to host plague reservoirs. The most recent study on the area highlights the proximity of plague foci to salt water, either the Mediterranean Sea, Atlantic Ocean or importantly inland salt lakes (Malek et al, 2016). These inland salt springs, called chotts, are saltier than the ocean. They were specifically able to cultivate Y. pestis from high salt soil and isolate a high salt tolerant strain of Yersinia pestis from Algeria. Plague foci across North Africa were found at an average of 0.89 km from salt water, while the average distance from fresh water is 4.6 km.

Plague sites 1940-2015. Red = plague sites, Blue = salt water lakes, Yellow = fresh water. Cropped from Malek et al, 2016.

They also note the importance of L-form Yersinia pestis in their environmental samples. L-form bacteria are an understudied cell wall deficient state that quite a few bacteria, including Yersinia pestis, use for long term survival. The L-form of Y. pestis may be important in environmental persistence. Because they are believed to have a slower reproduction rate,  the L-form may also play a role in altering the molecular clock of some strains. To date,  publications that focus on L-form Y. pestis have been in either Russian or Chinese. It seems clear that the L-form is found in some instances in Asia as well. Importantly, some L-form bacteria can regain their cell wall and return to active ‘normal’ growth.

Soil osmolarity is the key feature that allows (or requires) the L-form to persist. Withstanding osmotic tensions is the primary role of the cell wall. Without the cell wall, the cell loses its ‘normal’ shape, taking on a spherical shape determined by hydrophobic-hydrophilic interactions (like oil and water). As the cell membrane is primarily made of phospholipid, its the L-form shape resembles a sturdy oil globule or a liposome (B below). This was apparent by gram stain when the normal individual short rod-shaped (coccobacilli) cells transformed into clusters of completely round (cocci) cells. This was confirmed under the electron microscope where the change is very apparent.


They also isolated a strain, Algeria3, a descendant of the third pandemic, from soil containing 4% salt, that can grow in a 15% salt broth. Other Algerian isolates that were not found in high salt soils experimentally survived as well in high salt media if the salt content was ramped up in a step-wise fashion. Growth in high salt conditions altered their protein production to increase those related to osmoregulation, metabolism, outer membrane proteins and others of unknown function.  Osmoregulation genes changes are a direct response to the higher salt concentration. The L-form cells are clearly still metabolically active.

Taken together these protein profiles suggest that it has adapted to survive in the salty soil with the ability to adjust its structure and function as necessary to persist.  They note that other plague reservoirs are in regions of the world with salt lakes or other salty sources, but more environmental sampling will be necessary to determine if this is a universal Y. pestis capability. This all has obviously important implications for plague ecology.


Malek, M. A., Bitam, I., Levasseur, A., Terras, J., Gaudart, J., Azza, S., et al. (2016). Yersinia pestis halotolerance illuminates plague reservoirs. Scientific Reports, 7, 1–10.

Ötzi’s Lyme Disease in Context

One of the ancient DNA finds that continues to intrigue me is the discovery of Borrelia burgdorferi, the agent of Lyme disease, in Ötzi the 5300-year-old ice mummy from the Italian Alps. As far as I know, this is the only finding of B. burgdorferi in ancient remains of any date.  I discussed the initial report of these findings back in the summer of 2012. 


The more we learn about Ötzi’s environment and lifestyle, the less mysterious it seems. There are no signs of human habitation or land management in these high Alpine regions. Indicators of deforestation, farming, and pasture maintenance are lacking from lake sediment and pollen studies. Festi, Putzer and Oeggl (2013) found the first signs of human land management in the Ötztal Alps to began about 1000 years after Ötzi’s time. During the Copper Age, subsistence occupation of the valley floor was sufficient for the population of Ötzi’s time. They did minimal farming, and breeding of caprines (sheep, goats, and ibex). Festi, Putzer and Oeggl (2013) note that Ötzi’s mummy is the only piece of evidence for humans that high in the Otztal Alps before the Bronze Age.

Before Ötzi’s time, landscape management in the Mesolithic was to support red deer herds that were “in a state of semi-domestication by means of active hunting” (Rollo et al, 2002). (Native Americans managed deer populations in similar ways by promoting a landscape where deer thrive near their hunting grounds.) The importance of deer to Ötzi is underscored by everything about him from the red deer meat in his stomach to the roe deerskin that made up his quiver and antler in some of his tools (Rollo et al, 2012). Two different species of deer have been confirmed by genetic analysis.  Most of his clothing was made of sheep and goat skins (O’Sullivan et al, 2016).

The agent of Lyme disease, B. burgdorferi, is transmitted primarily by the tick Ixodes ricinus, common on deer, sheep, cattle, humans and dogs as adults and feed on rodents and small mammals as nymphs. Ticks often thrive at the forest edge where there are grasses for them to climb up to catch passing deer. It seems likely that they would also thrive in along upland forest edges as well. Ixodes ricinus is found throughout the Alps.  It is feasible that Lyme disease was a greater problem for humans when we relied on deer as a staple food.

Ötzi’s B. burgdorferi has yet to be confirmed by a second group. Interestingly, a recent study of B. burgdorferi’s phylogeny suggests that it originated in Europe and later spread to ‘post-Columbian’ North America (Margos et al, 2008). Although Lyme disease was only recognized in the 20th century, it is apparently an ancient disease caused by multiple Borrelia species. And Ötzi’s sequence has not been added to any phylogeny I’ve found, odd. Overlooked, or a problematic sequence?


Festi, D., Putzer, A., & Oeggl, K. (2013). Mid and late Holocene land-use changes in the Otztal Alps, territory of the Neolithic Iceman “Otzi”. Quaternary International, 353, 1–18.

Margos, G., Gatewood, A. G., Aanensen, D. M., Hanincová, K., Terekhova, D., Vollmer, S. A., et al. (2008). MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proceedings of the National Academy of Sciences, 105(25), 8730–8735.

O’Sullivan, N. J., Teasdale, M. D., Mattiangeli, V., Maixner, F., Pinhasi, R., Bradley, D. G., & Zink, A. (2016). A whole mitochondria analysis of the Tyrolean Iceman’s leather provides insights into the animal sources of Copper Age clothing. Scientific Reports, 6, 1–9.

Rollo, F., Ubaldi, M., Ermini, L., & Marota, I. (2002). Otzi’s last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proceedings of the National Academy of Sciences of the United States of America, 99(20), 12594–12599.