Molecular insights into the history of plague

Because of the limits inherent in historical sources on ancient plague epidemics, many questions concerning their etiology and epidemiology remain unanswered. Molecular biology tools and the use of dental pulp as a preserved source of bacterial DNA enabled us to demonstrate that Yersinia pestis was the etiologic agent of the 1347 European Black Death and of two additional epidemics in 1590 and 1722 in southern France.     

Validation of Inverse Seasonal Peak Mortality in Medieval Plagues,Including the Black Death,in Comparison to Modern Yersinia pestis-Variant Diseases

Background

Recent studies have noted myriad qualitative and quantitative inconsistencies between the medieval Black Death (and subsequent “plagues”) and modern empirical Y. pestis plague data, most of which is derived from the Indian and Chinese plague outbreaks of A.D. 1900±15 years. Previous works have noted apparent differences in seasonal mortality peaks during Black Death outbreaks versus peaks of bubonic and pneumonic plagues attributed to Y. pestis infection, but have not provided spatiotemporal statistical support. Our objective here was to validate individual observations of this seasonal discrepancy in peak mortality between historical epidemics and modern empirical data.

Methodology/Principal Findings

We compiled and aggregated multiple daily, weekly and monthly datasets of both Y. pestis plague epidemics and suspected Black Death epidemics to compare seasonal differences in mortality peaks at a monthly resolution. Statistical and time series analyses of the epidemic data indicate that a seasonal inversion in peak mortality does exist between known Y. pestis plague and suspected Black Death epidemics. We provide possible explanations for this seasonal inversion.

Conclusions/Significance

These results add further evidence of inconsistency between historical plagues, including the Black Death, and our current understanding of Y. pestis-variant disease. We expect that the line of inquiry into the disputed cause of the greatest recorded epidemic will continue to intensify. Given the rapid pace of environmental change in the modern world, it is crucial that we understand past lethal outbreaks as fully as possible in order to prepare for future deadly pandemics.     

Paläogenetik der Pest

Paleogenetics of the plague Plague has been part of our history since ancient times. Introduced again and again to Europe over centuries, the 'pestilences' killed millions of people before disappearing from the continent in 19^th Century. In the Middle Ages, bacteria were unknown and often the transmission routes of plague remained unrecognized. Plague was considered as a punishment by God disseminated by Miasma. With modern methods, microbiologists and palaeogenetists have now successfully shown that all the three historical recognized plague pandemics indeed were caused by the bacterium Yersinia pestis. In addition, important information has been obtained about the evolution of the bacterium and its origin. New data from ongoing studies on victims of the past epidemics help to shed new light on the past and perhaps even on the present of plague.     

The Black Death in Hereford,England: A demographic analysis of the Cathedral 14th-century plague mass graves and associated parish cemetery

Objectives

This study explores the paleoepidemiology of the Black Death (1348–52 AD) mass graves from Hereford, England, via osteological analysis. Hereford plague mortality is evaluated in the local context of the medieval city and examined alongside other Black Death burials.

Methods

The Hereford Cathedral site includes mass graves relating to the Black Death and a 12th-16th century parish cemetery. In total, 177 adult skeletons were analyzed macroscopically: 73 from the mass graves and 104 from the parish cemetery. Skeletal age-at-death was assessed using transition analysis, and sex and stress markers were analyzed.

Results

The age-at-death distributions for the mass graves and parish cemetery were significantly different (p = 0.0496). Within the mass graves, young adults (15–24 years) were substantially over-represented, and mortality peaked at 25–34 years. From 35 years of age onwards, there was little variation in the mortality profiles for the mass graves and parish cemetery. Males and females had similar representation across burial types. Linear enamel hypoplasia was more prevalent within the mass graves (p = 0.0340) whereas cribra orbitalia and tibial periostitis were underrepresented.

Conclusions

Mortality within the Hereford mass graves peaked at a slightly older age than is seen within plague burials from London, but the overall profiles are similar. This demonstrates that young adults were disproportionately at risk of dying from plague compared with other age groups. Our findings regarding stress markers may indicate that enamel hypoplasia is more strongly associated with vulnerability to plague than cribra orbitalia or tibial periostitis.     

The temporal dynamics of the fourteenth-century Black Death: new evidence from English ecclesiastical records

Recent research has questioned whether the European Black Death of 1347-1351 could possibly have been caused by the bubonic plague bacillus Yersinia pestis, as has been assumed for over a century. Central to the arguments both for and against involvement of Y. pestis has been a comparison of the temporal dynamics observed in confirmed outbreaks of bubonic plague in early-20th-century India, versus those reconstructed for the Black Death from English church records--specifically, from lists of institutions (appointments) to vacated benefices contained in surviving bishops' registers. This comparison is, however, based on a statistical error arising from the fact that most of the bishops' registers give only the dates of institution and not the dates of death. Failure to correct for a distributed (as opposed to constant) lag time from death to institution has made it look as if the Black Death passed slowly through specific localities. This error is compounded by a failure to disaggregate the information from the bishops' registers to a geographical level that is genuinely comparable to the modern data. A sample of 235 deaths from the bishop's register of Coventry and Lichfield, the only English register to list both date of death and date of institution, shows that the Black Death swept through local areas much more rapidly than has previously been thought. This finding is consistent with those of earlier studies showing that the Black Death spread too rapidly between locales to have been a zoonosis such as bubonic plague. A further analysis of the determinants of the lag between death and institution, designed to provide a basis for reexamining other bishops' registers that do not provide information on date of death, shows that the distribution of lags could vary significantly by time and space even during a single epidemic outbreak.     

Role of the Yersinia pestis yersiniabactin iron acquisition system in the incidence of flea-borne plague

Plague is a flea-borne zoonosis caused by the bacterium Yersinia pestis. Y. pestis mutants lacking the yersiniabactin (Ybt) siderophore-based iron transport system are avirulent when inoculated intradermally but fully virulent when inoculated intravenously in mice. Presumably, Ybt is required to provide sufficient iron at the peripheral injection site, suggesting that Ybt would be an essential virulence factor for flea-borne plague. Here, using a flea-to-mouse transmission model, we show that a Y. pestis strain lacking the Ybt system causes fatal plague at low incidence when transmitted by fleas. Bacteriology and histology analyses revealed that a Ybt-negative strain caused only primary septicemic plague and atypical bubonic plague instead of the typical bubonic form of disease. The results provide new evidence that primary septicemic plague is a distinct clinical entity and suggest that unusual forms of plague may be caused by atypical Y. pestis strains.     

Exposure of small rodents to plague during epizootics in black-tailed prairie dogs

Plague, caused by the bacterium Yersinia pestis, causes die-offs of colonies of prairie dogs (Cynomys ludovicianus). It has been argued that other small rodents are reservoirs for plague, spreading disease during epizootics and maintaining the pathogen in the absence of prairie dogs; yet there is little empirical support for distinct enzootic and epizootic cycles. Between 2004 and 2006, we collected blood from small rodents captured in colonies in northern Colorado before, during, and for up to 2 yr after prairie dog epizootics. We screened 1,603 blood samples for antibodies to Y. pestis, using passive hemagglutination and inhibition tests, and for a subset of samples we cultured blood for the bacterium itself. Of the four species of rodents that were common in colonies, the northern grasshopper mouse (Onychomys leucogaster) was the only species with consistent evidence of plague infection during epizootics, with 11.1-23.1% of mice seropositive for antibody to Y. pestis during these events. Seropositive grasshopper mice, thirteen-lined ground squirrels (Spermophilus tridecemlineatus), and deer mice (Peromyscus maniculatus) were captured the year following epizootics. The appearance of antibodies to Y. pestis in grasshopper mice coincided with periods of high prairie dog mortality; subsequently, antibody prevalence rates declined, with no seropositive individuals captured 2 yr after epizootics. We did not detect plague in any rodents off of colonies, or on colonies prior to epizootics, and found no evidence of persistent Y. pestis infection in blood cultures. Our results suggest that grasshopper mice could be involved in epizootic spread of Y. pestis, and possibly, serve as a short-term reservoir for plague, but provide no evidence that the grasshopper mouse or any small rodent acts as a long-term, enzootic host for Y. pestis in prairie dog colonies.     

High throughput, multiplexed pathogen detection authenticates plague waves in medieval Venice, Italy

Background

Historical records suggest that multiple burial sites from the 14th–16^th centuries in Venice, Italy, were used during the Black Death and subsequent plague epidemics.

Methodology/Principal Findings

High throughput, multiplexed real-time PCR detected DNA of seven highly transmissible pathogens in 173 dental pulp specimens collected from 46 graves. Bartonella quintana DNA was identified in five (2.9%) samples, including three from the 16th century and two from the 15th century, and Yersinia pestis DNA was detected in three (1.7%) samples, including two from the 14th century and one from the 16th century. Partial glpD gene sequencing indicated that the detected Y. pestis was the Orientalis biotype.

Conclusions

These data document for the first time successive plague epidemics in the medieval European city where quarantine was first instituted in the 14th century.     

Abandonment of farmland and vegetation succession following the Eurasian plague pandemic of ad 1347–52

Aim This paper reviews the available documentary, archaeological and palaeoecological evidence for the abandonment of agricultural land and consequent regeneration of the forest in Europe after the Black Death. Location Western and northern Europe. Methods This review is the result of an exhaustive search of the historical, archaeological and palaeoecological literature for evidence indicating agricultural decline and forest regeneration in Eurasia during the 14th century. The available evidence for landscape change can be divided into two categories: (1) documentary and archaeological sources, and (2) palaeoecological reconstructions of past vegetation. In the past few years, several pollen diagrams from north‐west Europe have been reported with precise chronologies (decadal and even annual scale) showing the abandonment of farmland and consequent ecological change in the late medieval period. Results and main conclusions There is strong evidence of agricultural continuity at several sites in Western Europe at the time of the Black Death. The effects of the Black Death on the European rural landscape varied geographically, with major factors probably including the impact of the plague on the local population, and soil quality. At two sites in western and northern Ireland, the late medieval decline in cereal agriculture was probably a direct result of population reduction following the Black Death. In contrast, the decline in cereal production began at sites in Britain and France before the Black Death pandemic of ad 1347–52, and was probably due to the crisis in the agricultural economy, exacerbated by political instability and climate deterioration. Much of the abandoned arable land was probably exploited for grazing during the period between the decline in cereal farming and the Black Death. In the aftermath of the Black Death, grazing pressure was greatly reduced owing to reductions in the grazing animal population and a shortage of farmers. Vegetation succession on the abandoned grazing land resulted in increased cover of woody tree species, particularly Betula and Corylus, by the late 14th century. The cover of woodland was greatest at c.ad 1400, before forest clearance and agriculture increased in intensity.     

Historical Epidemics Cartography Generated by Spatial Analysis: Mapping the Heterogeneity of Three Medieval "Plagues" in Dijon

Objectives

This work was designed to adapt Geographical Information System-based spatial analysis to the study of historical epidemics. We mapped "plague" deaths during three epidemics of the early 15th century, analyzed spatial distributions by applying the Kulldorff''s method, and determined their relationships with the distribution of socio-professional categories in the city of Dijon.

Materials and Methods

Our study was based on a database including 50 annual tax registers (established from 1376 to 1447) indicating deaths and survivors among the heads of households, their home location, tax level and profession. The households of the deceased and survivors during 6 years with excess mortality were individually located on a georeferenced medieval map, established by taking advantage of the preserved geography of the historical center of Dijon. We searched for clusters of heads of households characterized by shared tax levels (high-tax payers, the upper decile; low-tax payers, the half charged at the minimum level) or professional activities and for clusters of differential mortality.

Results

High-tax payers were preferentially in the northern intramural part, as well as most wealthy or specialized professionals, whereas low-tax payers were preferentially in the southern part. During two epidemics, in 1400–1401 and 1428, areas of higher mortality were found in the northern part whereas areas of lower mortality were in the southern one. A high concentration of housing and the proximity to food stocks were common features of the most affected areas, creating suitable conditions for rats to pullulate. A third epidemic, lasting from 1438 to 1440 had a different and evolving geography: cases were initially concentrated around the southern gate, at the confluence of three rivers, they were then diffuse, and ended with residual foci of deaths in the northern suburb.

Conclusion

Using a selected historical source, we designed an approach allowing spatial analysis of urban medieval epidemics. Our results fit with the view that the 1400–1401 epidemic was a Black Death recurrence. They suggest that this was also the case in 1428, whereas in 1438–1440 a different, possibly waterborne, disease was involved.     

Molecular and physiological insights into plague transmission, virulence and etiology

Plague is caused by Yersinia pestis, which evolved from the enteric pathogen Y. pseudotuberculosis, which normally causes a chronic and relatively mild disease. Y. pestis is not only able to parasitize the flea but also highly virulent to rodents and humans, causing epidemics of a systemic and often fatal disease. Y. pestis could be used as a bio-weapon and for bio-terrorism. It uses a number of strategies that allow the pathogen to change its lifestyle rapidly to survive in fleas and to grow in the mammalian hosts. Extensive studies reviewed here give an overall picture of the determinants responsible for plague pathogenesis in mammalians and the transmission by fleas. The availability of multiple genomic sequences and more extensive use of genomics and proteomics technologies should allow a comprehensive dissection of the complex of host-adaptation and virulence in Y. pestis.     

鼠疫的发病机制研究进展

鼠疫是由鼠疫耶尔森菌(Yersinia pestis，Y. pestis)感染引起的一种人畜共患病。鼠疫在世界范围内出现过3次大流行，均引起致命的瘟疫。由于自然疫源面积不断扩大和人口流动愈加频繁，我国的鼠疫防治形势依旧严峻。本文就鼠疫耶尔森菌的毒力因子、对宿主细胞的黏附和侵袭、胞内繁殖、宿主内播散等机制的研究进展进行总结，有助于揭示鼠疫独特的致病和传播机制，为精准防治鼠疫提供工作基础。     

Flea diversity as an element for persistence of plague bacteria in an East African plague focus

Plague is a flea-borne rodent-associated zoonotic disease that is caused by Yersinia pestis and characterized by long quiescent periods punctuated by rapidly spreading epidemics and epizootics. How plague bacteria persist during inter-epizootic periods is poorly understood, yet is important for predicting when and where epizootics are likely to occur and for designing interventions aimed at local elimination of the pathogen. Existing hypotheses of how Y. pestis is maintained within plague foci typically center on host abundance or diversity, but little attention has been paid to the importance of flea diversity in enzootic maintenance. Our study compares host and flea abundance and diversity along an elevation gradient that spans from low elevation sites outside of a plague focus in the West Nile region of Uganda (~725-1160 m) to higher elevation sites within the focus (~1380-1630 m). Based on a year of sampling, we showed that host abundance and diversity, as well as total flea abundance on hosts was similar between sites inside compared with outside the plague focus. By contrast, flea diversity was significantly higher inside the focus than outside. Our study highlights the importance of considering flea diversity in models of Y. pestis persistence.     

Plague mortality and demographic depression in later medieval England.

Both direct and indirect evidence implies that England experienced a lengthy period of stagnant or declining population during the later fourteenth and fifteenth centuries. The Black Death of 1348-1349 had brought about profound changes in England''s agrarian economy, and this subsequent demographic depression is most commonly interpreted by historians as the result of plague mortality, recurring in severe outbreaks after the disease''s introduction into the country. This paper reviews the evidence and assumptions behind this interpretation, in light of recent research by historical demographers and epidemiologists into bubonic plague epidemics and general mortality crises during the post-medieval period.     

Prevalence of Yersinia pestis in rodents and fleas associated with black-tailed prairie dogs (Cynomys ludovicianus) at Thunder Basin National Grassland, Wyoming

Rodents (and their fleas) that are associated with prairie dogs are considered important for the maintenance and transmission of the bacterium (Yersinia pestis) that causes plague. Our goal was to identify rodent and flea species that were potentially involved in a plague epizootic in black-tailed prairie dogs at Thunder Basin National Grassland. We collected blood samples and ectoparasites from rodents trapped at off- and on-colony grids at Thunder Basin National Grassland between 2002 and 2004. Blood samples were tested for antibodies to Y. pestis F-1 antigen by a passive hemagglutination assay, and fleas were tested by a multiplex polymerase chain reaction, for the presence of the plague bacterium. Only one of 1,421 fleas, an Oropsylla hirsuta collected in 2002 from a deer mouse, Peromyscus maniculatus, tested positive for Y. pestis. Blood samples collected in summer 2004 from two northern grasshopper mice, Onychomys leucogaster, tested positive for Y. pestis antibodies. All three positive samples were collected from on-colony grids shortly after a plague epizootic occurred. This study confirms that plague is difficult to detect in rodents and fleas associated with prairie dog colonies, unless samples are collected immediately after a prairie dog die-off.     

No evidence of persistent Yersina pestis infection at prairie dog colonies in north-central Montana

Sylvatic plague is a flea-borne zoonotic disease caused by the bacterium Yersinia pestis, which can cause extensive mortality among prairie dogs (Cynomys) in western North America. It is unclear whether the plague organism persists locally among resistant host species or elsewhere following epizootics. From June to August 2002 and 2003 we collected blood and flea samples from small mammals at prairie dog colonies with a history of plague, at prairie dog colonies with no history of plague, and from off-colony sites where plague history was unknown. Blood was screened for antibody to Y. pestis by means of enzyme-linked immunosorbent assay or passive hemagglutination assay and fleas were screened for Y. pestis DNA by polymerase chain reaction. All material was negative for Y. pestis including 156 blood samples and 553 fleas from colonies with a known history of plague. This and other studies provide evidence that Y. pestis may not persist at prairie dog colonies following an epizootic.     

Comparative genomics of 2009 seasonal plague (Yersinia pestis) in New Mexico

Plague disease caused by the gram-negative bacterium Yersinia pestis routinely affects animals and occasionally humans, in the western United States. The strains native to the North American continent are thought to be derived from a single introduction in the late 19(th) century. The degree to which these isolates have diverged genetically since their introduction is not clear, and new genomic markers to assay the diversity of North American plague are highly desired. To assay genetic diversity of plague isolates within confined geographic areas, draft genome sequences were generated by 454 pyrosequencing from nine environmental and clinical plague isolates. In silico assemblies of Variable Number Tandem Repeat (VNTR) loci were compared to laboratory-generated profiles for seven markers. High-confidence SNPs and small Insertion/Deletions (Indels) were compared to previously sequenced Y. pestis isolates. The resulting panel of mutations allowed clustering of the strains and tracing of the most likely evolutionary trajectory of the plague strains. The sequences also allowed the identification of new putative SNPs that differentiate the 2009 isolates from previously sequenced plague strains and from each other. In addition, new insertion points for the abundant insertion sequences (IS) of Y. pestis are present that allow additional discrimination of strains; several of these new insertions potentially inactivate genes implicated in virulence. These sequences enable whole-genome phylogenetic analysis and allow the unbiased comparison of closely related isolates of a genetically monomorphic pathogen.     

Tree-ring growth shows that the significant population decline in Norway began decades before the Black Death

The Black Death (1349–1350 in Norway) is often cited as the cause of a severe population decline and building hiatus in the middle of the 14th century. This paper analyses this hypothesis by matching the Black Death with human and environmental impacts on tree-ring growth. The number of buildings dated by dendrochronology in Norway shows a dramatic decline several decades before the plague. In Norway, the building hiatus, which has parallels in several other places in Europe, dates from the late-13th century almost to the 16th century. The first dated houses built after the plague date from the 15th century and many of the logs have exceptionally wide tree rings compared to timber from other periods. Assuming the rapid growth was because of an open landscape, the trees are likely to have grown on infields of farms abandoned due to the 14th century population decline. Since many of these fast-growing trees germinated in the early-14th century and the number of dated buildings drops dramatically several decades before the plague, the Black Death can hardly be the only reason for the population decline in Norway and one plausible explanation is that some environmental impact occurred decades earlier. The dendroclimatological evidence of cold and wet summers in the years before the plague is suggestive, but historical sources also pinpoint famine due to crop failure. They also tell of farms being abandoned several decades before the plague and mention periods of heavy rainfall and famine in the early-14th century.     

Yersinia--flea interactions and the evolution of the arthropod-borne transmission route of plague

Yersinia pestis, the causative agent of plague, is unique among the enteric group of Gram-negative bacteria in relying on a blood-feeding insect for transmission. The Yersinia-flea interactions that enable plague transmission cycles have had profound historical consequences as manifested by human plague pandemics. The arthropod-borne transmission route was a radical ecologic change from the food-borne and water-borne transmission route of Yersinia pseudotuberculosis, from which Y. pestis diverged only within the last 20000 years. Thus, the interactions of Y. pestis with its flea vector that lead to colonization and successful transmission are the result of a recent evolutionary adaptation that required relatively few genetic changes. These changes from the Y. pseudotuberculosis progenitor included loss of insecticidal activity, increased resistance to antibacterial factors in the flea midgut, and extending Yersinia biofilm-forming ability to the flea host environment.     

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called 'genetically monomorphic bacteria'. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus, whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis. Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894.