Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

Bos, Kirsten I.; Herbig, Alexander; Sahl, Jason W.; Waglechner, Nicholas; Fourment, Mathieu; Forrest, Stephen; Klunk, Jennifer; Schuenemann, Verena J.; Poinar, Debi; Kuch, Melanie; Golding, Brian; Dutour, Olivier; Keim, Paul; Wagner, David M.; Holmes, Edward C.; Krause, Johannes; Poinar, Hendrik N.

doi:10.1101/036509

Cited by 33 publications

(79 citation statements)

References 34 publications

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“…However, where did branch 1 itself continue to evolve? It has been suggested that a considerable part of that evolution, possibly for hundreds of years, was also in local reservoirs in Europe, with subsequent seeding of the 1.ANT populations in East and Central Africa followed by the 1.IN populations in China [32,34,36]. Alternately, that evolution might have continued in China and central Asia, with occasional epidemic sweeps that seeded Europe and East Africa [30].…”

Section: (A) Populations and Phylogenymentioning

confidence: 99%

“…The reconstruction of ancient genomes have indicated that 1.PRE1 (figure 2a) caused the Black Death in London [33] as well as other medieval outbreaks in continental Europe [34,37]. A descendant of these bacteria, 1.PRE1B, which had accumulated 20 nucleotide substitutions (SNV), was isolated from Ellwangen, Germany (1485-1627) [34], and 1.PRE1A, a further descendant population with about 60 additional informative SNVs, caused plague in Marseille in 1722 [36], almost 400 years after the Black Death. Bacteria that are related to 1.PRE by low-resolution SNP genotyping were also isolated in Germany in the fourteenth and seventeenth centuries [35].…”

Section: (A) Populations and Phylogenymentioning

confidence: 99%

“…Branches and populations within that tree that are defined by extant diversity have already been assigned characteristic names [16,30,48], for example branch 0 for the ancestral branch leading from [30], [16] and [31], including additional ancient genomes and genotypes (see below), plus proposed mnemonics for those populations. Sources of ancient genomes and genotypes: the Bronze Age (0.PRE1, 0.PRE2; grey) [31], the Justinianic Pandemic (0.ANT4; blue) [32]; the Black Death (1.PRE1; maroon; London, 1348 [33]; Barcelona 1300-1420 [34]; SNP-based genotypes from Germany (fourteenth and seventeenth centuries) [35]) and descendent branches of 1.PRE from Ellwangen (1.PRE1B; 1485-1627) [34] and Marseille (1.PRE1.A, 1722) [36]). One SNP further along branch 1 are the populations 1.PRE2 (London, 1362-1400 [36] and the related low-resolution genotype found in Berg-Op-Zoom, The Netherlands from the fourteenth century [37]; green).…”

Section: (A) Populations and Phylogenymentioning

confidence: 99%

“…Sources of ancient genomes and genotypes: the Bronze Age (0.PRE1, 0.PRE2; grey) [31], the Justinianic Pandemic (0.ANT4; blue) [32]; the Black Death (1.PRE1; maroon; London, 1348 [33]; Barcelona 1300-1420 [34]; SNP-based genotypes from Germany (fourteenth and seventeenth centuries) [35]) and descendent branches of 1.PRE from Ellwangen (1.PRE1B; 1485-1627) [34] and Marseille (1.PRE1.A, 1722) [36]). One SNP further along branch 1 are the populations 1.PRE2 (London, 1362-1400 [36] and the related low-resolution genotype found in Berg-Op-Zoom, The Netherlands from the fourteenth century [37]; green). One further SNP down the branch is a short branch leading to a genome from Western Asia (1.PRE3; Bolgar City, Tatarstan, Russia; light blue) [34].…”

Section: (A) Populations and Phylogenymentioning

confidence: 99%

“…The direct descent along branch 1 is marked after one SNP by 1.PRE2. 1.PRE2 was isolated from London in the decades after the Black Death [36] and its close relatives, according to SNP typing, were isolated from plague deaths from the fourteenth century in The Netherlands [37]. 1.PRE3 designates a population that is one further SNP along branch 1; its genome was obtained from a mass grave in Bolgar City, Tatarstan, Russia (1362-1400) [34].…”

Section: (A) Populations and Phylogenymentioning

confidence: 99%

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How old are bacterial pathogens?

Achtman¹

2016

Proc. R. Soc. B.

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Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori , which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis , the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis . Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases.

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Section: (A) Populations and Phylogenymentioning

confidence: 99%

Section: (A) Populations and Phylogenymentioning

confidence: 99%

Section: (A) Populations and Phylogenymentioning

confidence: 99%

Section: (A) Populations and Phylogenymentioning

confidence: 99%

Section: (A) Populations and Phylogenymentioning

confidence: 99%

See 3 more Smart Citations

How old are bacterial pathogens?

Achtman¹

2016

Proc. R. Soc. B.

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Stress, sex, and plague: Patterns of developmental stress and survival in pre‐ and post‐Black Death London

DeWitte

2017

American J Hum Biol

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Objectives: Previous research revealed declines in survivorship in London before the Black Death (c. 1346Death (c. -1353, and improvements in survivorship following the epidemic. These trends indicate that there were declines in general levels of health before the Black Death and improvements thereof afterwards. This study expands on previous research by examining whether changes in survivorship were consistent between the sexes, and how patterns of developmental stress markers changed before and after the Black Death. Materials and Methods:This study uses samples from London cemeteries dated to one of three periods: Early Pre-Black Death (1000-1200 AD, n 5 255), Late PreBlack Death (1200-1250 AD, n 5 247), or Post-Black Death (1350-1540 AD n 5 329). Temporal trends in survivorship are assessed via Kaplan-Meier survival analysis, and trends in tibial length (as a proxy for stature) and linear enamel hypoplasia (LEH) are assessed using t-tests and Chi-square tests, respectively.Results: Survivorship for both sexes decreased before the Black Death and increased afterwards. For males, LEH frequencies increased and stature decreased before the epidemic, and LEH declined and stature increased after the Black Death. For females, the only significant change with respect to developmental stress markers was a decrease in stature after the Black Death.Conclusions: These results might reflect variation between the sexes in sensitivity to stressors, the effects of nutrition on pubertal timing, disproportionate access to dietary resources for males in the aftermath of the Black Death, the disproportionate deaths of frail individuals during the epidemic, or some combination of these factors. | I NT ROD UCTI ONRecent research has yielded important insights about the 14 th -century Black Death, one of the most devastating epidemics in history and the first outbreak of what is often referred to as the Second Pandemic of Plague. Molecular evidence from 14 th -century Black Death burials confirms the long-held (though previously strongly contested) assumption that the Black Death was caused by Yersinia pestis, the bacterium that causes bubonic plague in living populations (Bos et al., 2011;Haensch et al., 2010;Kacki, Rahalison, Rajerison, Ferroglio, & Bianucci, 2011;Raoult et al., 2000;Schuenemann et al., 2011). There is also molecular evidence that Y. pestis infected individuals in the Bronze age (Rasmussen et al., 2015), during the 6 th -century AD Plague of Justinian (Harbeck et al., 2013;Wagner et al., 2014;Wiechmann & Grupe, 2005), and in outbreaks of plague subsequent to the Black Death in the medieval and early modern periods (Bos et al., 2016;Tran et al., 2011). Plague continues to kill people every year. During a recent outbreak in Madagascar, for example, there were nearly 500 reported cases and over 80 deaths (Bertherat, 2015). Plague has thus affected humans, at times severely, for over 5000 years.Despite the interest that plague has generated among generations of scholars from a variety of disciplines, some o...

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Calculus and survivorship in medieval London: The association between dental disease and a demographic measure of general health

Yaussy

DeWitte

2019

American J Phys Anthropol

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Objectives: Dental plaque is associated with a variety of systemic diseases and mortality risks in living populations. However, bioarchaeologists have not fully investigated the mortality risks associated with plaque (or its mineralized form, calculus) in the past. This study examines the relationship between survivorship and calculus in a medieval skeletal sample.Materials and methods: Our sample (n = 1,098) from four medieval London cemeteries, c. 1000-1540 CE, includes people who died under attritional (normal) and catastrophic (famine and plague) conditions. The associations between age and the presence of dental calculus on the permanent left first mandibular molar are assessed using binary logistic regression and Kaplan-Meier survival analysis. Results: The regression results indicate a significant negative relationship between age and calculus presence for individuals of all ages who died under normal mortality conditions and for adults who died under both normal and catastrophic conditions. Survival analysis reveals decreased survivorship for people of all ages with calculus under normal mortality conditions. Similarly, during conditions of catastrophic mortality, adult males with calculus suffered reduced survivorship compared to males without it, though there was no difference in survivorship between adult females with and without calculus. Conclusions: These results suggest that, as in modern populations, calculus accumulation in the inhabitants of medieval London reflects a greater risk of premature death. The evaluation of calculus, a potential measure of underlying frailty, in the context of a demographic measure of general health suggests that it might provide insights into health in past populations. K E Y W O R D S binary logistic regression, bioarchaeology, mortality, paleodemography, paleopathology, survival analysis

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Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

Abstract: Death. These data suggest the existence of a previously uncharacterized historical 35 plague focus that persisted for at least three centuries. We propose that this 36 disease source may have been responsible for the many resurgences of plague in

Cited by 33 publications

References 34 publications

How old are bacterial pathogens?

How old are bacterial pathogens?

Stress, sex, and plague: Patterns of developmental stress and survival in pre‐ and post‐Black Death London

Calculus and survivorship in medieval London: The association between dental disease and a demographic measure of general health

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