Category Archives: epidemiology

Landscapes of Disease Themed Issue

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For the last couple years, I have been writing about a landscape-based approach to the study of infectious disease in general and historic epidemics in particular. When I first wrote about Lambin et al.’s now classic paper “Pathogenic landscapes” nearly three years ago, I did not know then that it would be so influential in my thinking or that the Medieval Congress sessions would be so successful. In the fall of 2014, Graham Fairclough and I began talking about ways that this first congress session could be represented in the journal he edits, Landscapes. This issue is a departure from their usual approach to landscape studies so I would like to thank Graham Fairclough for entrusting me with a whole issue. It has been a challenge for both of us, and I am proud of our product.

This issue represents the wide variety of studies that can be done all contributing to an understanding of past landscapes of disease. One of the reasons why I like the phrase landscape of disease, rather than simply landscape epidemiology, is that it opens up the array of disciplines that can be involved. In the study of diseases of the past, humanistic approaches can be as valuable as scientific methods. Both are required to build a reasonably coherent reconstruction of the past. Science and the humanities need to act as a check and balance on each other, hopefully in a supportive and collegial way.

The issue was published online a couple days ago. Accessing the journal through your library will register interest in the journal with both your library and the publisher, and would be appreciated. By now the authors should (or will soon) have their codes for their free e-copies if you do not have access otherwise.

Table of Contents

Landscapes of Disease by Michelle Ziegler. An introduction to the concept of ‘landscapes of disease’ and the articles in the issue. (Open access)

The Diseased Landscape: Medieval and Early Modern Plaguescapes by Lori Jones

The Influence of Regional Landscapes on Early Medieval Health (c. 400-1200 A.D.): Evidence from Irish Human Skeletal Remains by Mara Tesorieri

Malarial Landscapes in Late Antique Rome and the Tiber Valley by Michelle Ziegler

Epizootic Landscapes: Sheep Scab and Regional Environment in England in 1279-1280 by Philip Slavin

Plague, Demographic Upheaval and Civilisational Decline: Ibn Khaldūn and Muḥammed al-Shaqūrī on the Black Death in North Africa and Islamic Spain by Russell Hopley

plus seven book reviews. Enjoy!


Lambin, E. F., Tran, A., Vanwambeke, S. O., Linard, C., & Soti, V. (2010). Pathogenic landscapes: Interactions between land, people, disease vectors, and their animal hosts. International Journal of Health Geographics, 9(1), 54.

The Case for Louse-Transmitted Plague

Louse illustration by Robert Hooke, Micrographia, 1667. (Public domain)

by Michelle Ziegler

The key to understanding plague — past, present, and future — has always been understanding its vector dynamics. By the latest tally, there are 269 known flea species, plus a small collection of ticks and lice, that can be infected with Yersinia pestis. With this many infected parasites, it’s not a surprise that 344 hosts have been identified (Dubyanskiy & Yeszhanov, 2016), but this list is still incomplete. (It does not include all of the minor hosts in North America.) Regardless, this is not a description of a picky pathogen! Unfortunately, it is far easier to identify infected hosts and potential vectors than to determine which of these insects are effective vectors and their transmission dynamics.

Numerous species of fleas have been identified as plague vectors in specific localities. However, only five infected potential human vectors are possibly involved in a wide distribution of human plague cases — the rat flea Xenopsylla cheopis, the cat flea Ctenocephalides felis, the human flea Pulex irritans,  the human body louse Pediculus humanus humanus, and the human head louse Pediculus humanus capitis. The rat flea and the cat flea are known vectors, but  they are unlikely to account for the full transmission of the massive first and second pandemics.  I recently discussed the possible role of the human flea. Given the worldwide distribution of human lice, they are attractive vectors but there is still work to do before they can be considered likely primary vectors for human to human transmission during the first two pandemics.

Raoult Makes his Case…again

Didier Raoult and his team have been working on plague and their louse transmission hypothesis for a long time.  It has already been ten years since they had enough information to write their first review article putting forth their human ectoparasite theory of plague transmission (Drancourt, Houhamdi, & Raoult, 2006).

At this point, their primary supporting evidence was some experiments with human louse plague transmission in rabbits (Houhamdi et al, 2006) and they thought they could associate louse transmission with an “Orientalis-like” biovar of Yersinia pestis they identified in the first two pandemics (Drancourt et al, 2004).  However, later ancient DNA work showed that the first two pandemics were caused by strains of Yersinia pestis that emerged before the Orientalis biovar. Genetic reclassification of Yersinia pestis has also made the biovars largely obsolete.  Tensions between groups working on ancient plague DNA developed quickly, and have been documented by historians Lester Little (2011) and Jim Bolton (2013).

This summer Didier Raoult (2016) restated his “personal view” on the role of lice in plague transmission. This essay is unusual not only as a first person narrative in science, including individual claims of discovery, but also for being so vindictive in its attack on his rivals. Again, see Little (2011) and Bolton (2013) for less biased accounts.  His team has done very impressive work.

His team has continued to assemble much of the work needed to argue that human lice were instrumental in at least some of the major human outbreaks of plague during the first two pandemics. Combing primarily French medical reports in North Africa, they were able to identify observations that suggest that lice were involved in some mid-twentieth century outbreaks (Raoult, 2016; Malak, Bitam, & Drancourt, 2016).  One of their most interesting findings in 2011 was the discovery of co-infection with Yersinia pestis and Bartonella quintana (trench fever) in late medieval French remains (Tran et al, 2011).  Trench fever is well known to be transmitted by the human louse. Both B. quintana and Y. pestis have been found in contemporary lice taken from plague patients in regions of endemic plague in the Congo (Piarroux et al, 2013; Drali et al, 2015). Unfortunately, neither of these studies mention the presence or absence of fleas.  That blood feeding lice would be infected is not a surprise, but the question of transmission stubbornly remains. There has yet to be a contemporary outbreak where all potential vectors, fleas and lice, were investigated. On a side note, the finding of widespread B. quintana is interesting, and perhaps a proxy for heavy lice infestation.

Modeling Transmission

In the meantime, while Raoult’s latest summary was in press, additional evidence was beginning to be revealed. Graduate student Katharine Dean of the MedPlag project in Oslo was modeling past epidemics for transmission by rat fleas, human lice, and pneumonic transmission. In her master’s thesis, she showed that lice transmission fits the second pandemic epidemics at Givry in 1348, London in 1563-64, and Florence in 1630-31 better than rat fleas or pneumonic transmission (Dean 2015). At the most recent Yersinia meeting in October, Dean presented a poster with expanded data finding outbreaks that fit each of these three modes of transmission (pneumonic in Manchuria, rat fleas in Sydney and Hong Kong, and lice in many locations) (Dean et al, 2016). Their work is still in progress and I’m sure many will be eager to see their results in due course.

Almost there

There are still a few lingering things to nail down. A modern outbreak investigation that looks at all ectoparasites, fleas and lice,  in the region that suggests lice are involved. It would be good to find lice (or fleas for that matter) in a plague burial that yields Y pestis aDNA. Alternatively, detection of more coinfection of Y. pestis with a louse-transmitted infection like B. quintana would lend additional support.  These findings will will require some good fortune. To differentiate between the human flea and lice, a better understanding of the pathology of a Y. pestis infection in the potential vector and its transmission dynamics is really needed. The models can’t differentiate human ectoparasites without more information.

Human ectoparasites are beginning to look much more likely especially for northern epidemics (Hufthammer & Walløe, 2013). More information is still needed to distinguish between human fleas and lice, although they may be both involved in different outbreaks.  We need to be ready for yet another paradigm change in plague history. Looking at the overall plague vector dynamics of the great pandemics, from sylvatic reservoir to distant human populations, is going to get a whole lot more complicated but also more interesting.


Bolton, J. L. (2013). Looking for Yersinia pestis: Scientists, Historians, and the Black Death. The Fifteenth Century, XII, 15–38.

Dean, K. R. (2015, June 1). Modeling plague transmission in Medieval European cities. (B. V. Schmid, Supervisor). Oslo. [Master’s Thesis]

Dean, K. R., Stenseth, N. C., Walløe, L., Lingærde, O. C., Bramanti, B., & Schmid, B. V. (2016, October). Human ectoparasites spread plague during the Black Death and Second Pandemic. Yersinia 12th International Symposium. Tbilisi, Georgia.

Drali, R., Shako, J. C., Davoust, B., Diatta, G., & Raoult, D. (2015). A New Clade of African Body and Head Lice Infected by Bartonella quintana and Yersinia pestis–Democratic Republic of the Congo. American Journal of Tropical Medicine and Hygiene, 93(5), 990–993.

Drancourt, M., Houhamdi, L., & Raoult, D. (2006). Yersinia pestis as a telluric, human ectoparasite-borne organism. The Lancet Infectious Diseases, 6(4), 234–241.

Drancourt, M., Roux, V., Dang, L. V., Tran-Hung, L., Castex, D., Chenal-Francisque, V., Ogata, H., Fournier, P-E., Crubezy, E, and  Raoult, D. (2004). Genotyping, Orientalis-like Yersinia pestis, and plague pandemics. Emerging Infectious Diseases, 10(9), 1585–1592.

Dubyanskiy, V. M., & Yeszhanov, A. B. (2016). Ecology of Yersinia pestis and the Epidemiology of Plague. Yersinia Pestis: Retrospective and Perspective, 918(Chapter 5), 101–170.

Houhamdi, L., Lepidi, H., Drancourt, M., & Raoult, D. (2006). Experimental model to evaluate the human body louse as a vector of plague. The Journal of Infectious Diseases, 194(11), 1589–1596.

Hufthammer, A. K., & Walløe, L. (2013). Rats cannot have been intermediate hosts for Yersinia pestis during medieval plague epidemics in Northern Europe. Journal of Archaeological Science, 40(4), 1752–1759.

Little, L. K. (2011). Plague Historians in Lab Coats. Past & Present, 213(1), 267–290.

Malek, M. A., Bitam, I., & Drancourt, M. (2016). Plague in Arab Maghreb, 1940–2015: A Review. Frontiers in Public Health, 4, 18–6.

Piarroux, R., Abedi, A. A., Shako, J. C., Kebela, B., Karhemere, S., Diatta, G., et al. (2013). Plague epidemics and lice, Democratic Republic of the Congo. Emerging Infectious Diseases, 19(3), 505–506.

Raoult, D. (2016). A Personal View of How Paleomicrobiology Aids Our Understanding of the Role of Lice in Plague Pandemics. Microbiology Spectrum, 4(4).

Drali, R., Mumcuoglu, K., & Raoult, D. (2016). Human Lice in Paleoentomology and Paleomicrobiology. Microbiology Spectrum, 4(4).

Tran, T.-N.-N., Forestier, C. L., Drancourt, M., Raoult, D., & Aboudharam, G. (2011). Brief communication: co-detection of Bartonella quintana and Yersinia pestis in an 11th-15th burial site in Bondy, France. American Journal of Physical Anthropology, 145(3), 489–494.

Rivers in European Plague Outbreak Patterns, 1347-1760

by Michelle Ziegler

The era of big data is coming to historic epidemiology. A new study published this month in Scientific Reports took a database of 5559 European outbreak reports (81.9% from UK, France and Germany) between 1347 and 1760 to analyze the role of rivers in the incidence and spread of plague. Their hypothesis was that river trade played a similar role as maritime trade in disseminating the plague but that the correlation would grow weaker over time as movement of goods over land became less expensive. In the 14th century, water transport was approximately ten times cheaper than land transport; the cost ratio diminishes to two to four times as expensive by the 18th century.  While it is not surprising that rivers had a role in disseminating the plague, the high correlation Yue, Lee, and Wu (2016) found between not only the proximity of the river but also its size and elevation is striking. Over 95% of the outbreaks occurred within 10 km of a ‘navigable’ river, defined as 5 m or greater in modern width and to differentiate maritime from riverine trade, excluded outbreak sites within 5 km of the maritime coastline. To ensure that rivers were suitable as trade routes, they only included rivers that linked two cities and excluded rivers that flowed into a lake without an outlet.

“Figure 1. Temporal and spatial distribution of plague outbreak in Europe in AD 1347–1760 (modifed from Büntgen et al 2012).” Yue, Lee, & Wu, 2016.

If we drill down into their results more directly, then we find that 84% of the city centers were less than 1 km from a river with 79.5% of those being on a river at least 20 meters wide. By their calculations, the average river width was 84.6 m. This correlates well with increased traffic and goods following to and through cities on substantial rivers. It is worth nothing here that the specific examples they give in England, Fossdyke, River Great Ouse, and the River Derwent are either canals or fit into an extensive canal system.

Looking at relationships between the outbreak sites and geography also favors high traffic river routes. When they included a “spatial lag in the regression models” they showed that there is a “highly significantly correlation with the spatial lag (p <0.01), indicating that plague outbreaks were spatially dependent upon previous outbreaks in adjacent cities” (Yu, Lee & Wu, p. 2). There was also a negative correlation between elevation and plague incidence, which they attribute to a lack of navigable rivers at higher elevations noting that only 20 incidents were recorded above 1000 m over sea level.  They also tested their results with controls for population density and economic status which did not effect their results for the likelihood of plague incidence or the association between outbreaks and river width. This will have to be evaluated by those with more modeling experience than I have.

There are a few caveats. First, such studies are only as good as their database. Yue, Lee and Wu used the digitized database constructed by Büntgen et al (2012) that was itself based on  a 35 year old archive published in French. I’ll leave its scrutiny to historians. They also do not address potential biases in all such databases, such as the likelihood that urban sites are recorded at a higher frequency than rural sites or that the political climate can effect the survival of records. Indeed, economic records are likely to note pestilence as a factor effecting commerce. While the environmental destruction of an enduring war could increase plague incidence, the high level of records from the ’30 years war’ needs a historians eye to evaluate. They also note that they are using measurements of modern rivers and canals that may have been significantly different in the past, modified by both natural processes such as silting or flooding and man-made changes such as straightening, dredging, or canal development.

They  also assume there were no European reservoirs, which we now know is not true. Ancient DNA studies have indicated that there were at least two strains descended from the Black Death circulating within late medieval Europe (Bos et al, 2016;  Spyrou et al, 2016). The European reservoir(s) have not yet been located. However, relatively few of the incidents reported in the database are likely to be actual zoonotic events linked directly to a local sylvatic (wild) reservoir, plus many known reservoirs outside of Europe are found at high elevation (for example in Tibet or Madagascar) and so are unlikely to be in this particular database given the absence of sites at higher elevations. Once a new outbreak emerges from a high elevation reservoir and comes off the mountain so to speak, then its transmissions by rivers is as likely as a strain entering from outside of Europe. On the other hand, if cities or even river networks are the actual reservoir, it would significantly effect their results.

River and canal networks or large river ports could function as reservoirs. River ports are similar to coastal maritime ports in that they have warfs, warehouses and nearby markets that would support large rodent populations. Barge traffic would specialize in transport of grain and other foodstuffs attractive to rodents.  Yue, Lee and Wu  (2016) state that they did not query their database for the effect of flooding because they could not accurately predict where floods would occur, that flooding is not predictable based solely on river width. Flooding along these river and canal systems is something that needs to be investigated because it would force rodents out of their normal shelter and could be related to human outbreaks (as the plague of 589 in Rome probably was). Floods could also carry infected rodents or fleas downstream on floating debris.

This study is a interesting jumping off point for future work. The database needs to be evaluated by historians and perhaps subdivided into smaller time periods. Division of the database into regional studies would also allow local archaeology and ecology to be more informative on precise outbreaks. I’m looking forward to all of questions big data studies like this one open up!


Yue, R. P. H., Lee, H. F., & Wu, C. Y. H. (2016). Navigable rivers facilitated the spread and recurrence of plague in pre-industrial Europe. Scientific Reports, 1–8.

Büntgen, U., Ginzler, C., Esperf, J., Tegel, W., & McMichael, A. J. (2012). Digitizing historical plague. Clinical Infectious Diseases, 55(11), 1586–1588.

Bos, K. I., Herbig, A., Sahl, J., Waglechner, N., Fourment, M., Forrest, S. A., et al. (2016). Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. eLife, 5, 17837.

Spyrou, M. A., Tukhbatova, R. I., Feldman, M., Drath, J., Kacki, S., de Heredia, J. B., et al. (2016). Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics. Cell Host and Microbe, 19(6), 874–881.