Advancing the understanding of treponemal disease in the past and present

Redefining the treponemal history through pre-Columbian genomes from Brazil

The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions1,2. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico3-6. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.

From the Ground Up: A Multidisciplinary Approach to Past Fertility and Population Narratives

Population dynamics form a crucial component of human narratives in the past. Population responses and adaptations not only tell us about the human past but also offer insights into the present and future. Though an area of substantial interest, it is also one of often limited evidence. As such, traditional techniques from demography and anthropology must be adapted considerably to accommodate the available archaeological and ethnohistoric data and an appropriate inferential framework must be applied. In this article, I propose a ground-up, multidisciplinary approach to the study of past population dynamics. Specifically, I develop an empirically informed path diagram based on modern fertility interactions and sources of past environmental, sociocultural, and biological evidence to guide high-resolution case studies. The proposed approach is dynamic and can evolve in response to data inputs as case studies are undertaken. In application, this approach will create new knowledge of past population processes which can greatly enhance our presently limited knowledge of high-frequency, small-scale demographic fluctuations, as well as contribute to our broader understanding of significant population disturbances and change throughout human history.

Technical note: The use and misuse of threshold diagnostic criteria in paleopathology

Weighted threshold diagnostic criteria approaches have emerged for diseases that involve skeletal/bony tissue that are readily diagnosed in the field of paleopathology such as Vitamin C deficiency (scurvy), Vitamin D deficiency (rickets) and treponemal disease. These criteria differ from traditional differential diagnosis in that they involve standardized inclusion criteria based on the lesion's specificity to the disease. Here I discuss the limitations and benefits of threshold criteria. I argue that while these criteria will benefit from further revision such as inclusion of lesion severity, and the incorporation of exclusion criteria, threshold diagnostic approaches have considerable value in the future of diagnosis in the field.

The Oral Health of a Group of 19th Century South Australian Settlers in Relation to Their General Health and Compared with That of Contemporaneous Samples

The aims of this study are to determine the oral health status of a rare sample of 19th-century migrant settlers to South Australia, how oral conditions may have influenced their general health, and how the oral health of this group compares with contemporaneous samples in Australia, New Zealand, and Britain. Dentitions of 18 adults and 22 subadults were investigated using non-destructive methods (micro-CT, macroscopic, radiographic). Extensive carious lesions were identified in seventeen adults and four subadults, and from this group one subadult and sixteen adults had antemortem tooth loss. Sixteen adults showed evidence of periodontal disease. Enamel hypoplastic (EH) defects were identified in fourteen adults and nine subadults. Many individuals with dental defects also had skeletal signs of comorbidities. South Australian individuals had the same percentage of carious lesions as the British sample (53%), more than other historic Australian samples, but less than a contemporary New Zealand sample. Over 50% of individuals from all the historic cemeteries had EH defects, suggesting systemic health insults during dental development were common during the 19th century. The overall oral health of the South Australian settlers was poor but, in some categories, (tooth wear, periapical abscess, periodontal disease), better than the other historic samples.

A paleoepidemiological approach to the challenging differential diagnosis of an isolated 1500-year-old anomalous molar from Panamá

OBJECTIVE

This study seeks to quantify the presence and prevalence of specific genetic and infectious diseases in the pre-Colombian Panamanian population and uses these data to consider the plausibility of these diseases as causative factors in the development of an abnormal supernumerary cusp morphology in a 1500-year-old isolated molar recovered from Cerro Juan Díaz (Los Santos, Panama).

MATERIALS

267 individuals from pre-Columbian sites throughout Panama.

METHODS

The anomalous tooth was analyzed through macroscopic, odontometric, and radiographic means. Tentative differential diagnosis was performed using inferences from paleopathological features of the broader regional population.

RESULTS

The regional sample showed evidence of treponemal infection and developmental anomalies in 10.1% and 10.9% of individuals, respectively.

CONCLUSIONS

While not able to rule out three potential genetic conditions, more evidence was found to support the differential diagnosis of congenital syphilis as the causative agent leading to the development of abnormal supernumerary cusps in the isolated molar.

SIGNIFICANCE

This study demonstrates how characterizing disease experience in the population can assist in differential diagnoses at the individual level and cautions against the assumption that any one lesion in isolation is unique to only one specific pathological condition.

LIMITATIONS

The timing discrepancy between clinical descriptions of congenital syphilis and genetic disorders, lack of knowledge on pathophysiological mechanisms of the former, poor preservation of Treponema pathogen ancient DNA, and deficiencies in modern public health data from Panama limit the differential diagnosis.

SUGGESTIONS FOR FURTHER RESEARCH

Inclusion and serious contemplation of genetic diseases in paleopathological differential diagnoses is necessary.

Twenty-first century bioarchaeology: Taking stock and moving forward

This article presents outcomes from a Workshop entitled "Bioarchaeology: Taking Stock and Moving Forward," which was held at Arizona State University (ASU) on March 6-8, 2020. Funded by the National Science Foundation (NSF), the School of Human Evolution and Social Change (ASU), and the Center for Bioarchaeological Research (CBR, ASU), the Workshop's overall goal was to explore reasons why research proposals submitted by bioarchaeologists, both graduate students and established scholars, fared disproportionately poorly within recent NSF Anthropology Program competitions and to offer advice for increasing success. Therefore, this Workshop comprised 43 international scholars and four advanced graduate students with a history of successful grant acquisition, primarily from the United States. Ultimately, we focused on two related aims: (1) best practices for improving research designs and training and (2) evaluating topics of contemporary significance that reverberate through history and beyond as promising trajectories for bioarchaeological research. Among the former were contextual grounding, research question/hypothesis generation, statistical procedures appropriate for small samples and mixed qualitative/quantitative data, the salience of Bayesian methods, and training program content. Topical foci included ethics, social inequality, identity (including intersectionality), climate change, migration, violence, epidemic disease, adaptability/plasticity, the osteological paradox, and the developmental origins of health and disease. Given the profound changes required globally to address decolonization in the 21st century, this concern also entered many formal and informal discussions.

Identifying treponemal disease in early East Asia

Objectives

Historic records suggest that a virulent form of treponematosis, sexually transmitted syphilis was introduced to Asia from Europe by the da Gama crew, who landed in India in 1498. Our objective is to assess the gross pathology of human skeletal remains from the Tang dynasty of China to test the presence of treponemal infection in East Asia before 1498. We interpret this paleopathological evidence in the context of site ecology and sociocultural changes during the Tang dynasty.

Materials and methods

We examined the gross pathology of 1598 human skeletons from Xingfulindai (AD 618 to AD 1279) archeological site located on the Central Plain of China. Using the modified diagnostic criteria defined by Hackett's classical work, we classify the pathology as consistent, strongly suggestive, or pathognomonic for treponemal infection.

Results

Twelve adult individuals from Xingfulindai had bone lesions suggestive of systemic pathology. Two of these individuals displayed a combination of lesion patterns pathognomonic of treponemal disease and one had lesions consistent with treponematosis. The radiocarbon dates for the bone samples from these skeletons place them before AD 1200.

Conclusions

The location of Xingfulindai in a continental climatic zone is not typical for yaws and bejel ecology, because these strains occur in the tropics, or in hot, dry environments, respectively. The urban setting, where there is documented evidence for increased interaction between multiple ethnic groups and a developed institution of courtesans during the Tang dynasty, favors sexually transmitted syphilis as the more likely diagnosis. This study supports an earlier spread of syphilis to China than 1498.

Was it worth migrating to the new British industrial colony of South Australia? Evidence from skeletal pathologies and historic records of a sample of 19th-century settlers

OBJECTIVES

To examine pathological evidence present in a sample of 19th -century settlers to South Australia in the context of an early industrial society.

MATERIALS

Skeletal remains of 20 adults and 45 nonadults from the government funded burial site (free ground) of St Mary's Anglican Church Cemetery, gravestones of privately funded burials and local parish records.

METHODS

Investigation of pathological manifestations of skeletal remains, church records and historic literature. Comparison with similar samples from Britain and from New South Wales.

RESULTS

Joint disease seen in 35% of adults. Porosity in bone cortices indicative of vitamin C deficiency seen in 32% of the total sample and porous lesions in the orbit (cribra orbitalia) in 7% of nonadults. Traumatic fractures identified in two adult males. Gastrointestinal conditions were the leading cause of death for nonadults, most adults died of pulmonary conditions. Life expectancy of people buried at the expense of the government was 23.8-42.6 years, those in private burials 57.1 years.

CONCLUSION

Health of migrant settlers from the St Mary's free ground did not differ much from that of a similar population in Britain nor of settlers in New South Wales. Thus, it is characteristic for lower socioeconomic groups in early industrialised societies.

SIGNIFICANCE

St Mary's sample is a rarity due scarcity of similar Australian skeletal samples.

LIMITATIONS

Small sample size and lack of similar samples for comparison.

SUGGESTIONS FOR FURTHER RESEARCH

Comprehensive investigation of dentitions in St Mary's sample and studies of more skeletal samples of early settlers in other Australian locations.

Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis

Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides.

A content analysis by bibliometry of the first ten years of the International Journal of Paleopathology

OBJECTIVES

The aim is to provide an overview of the nature of the content of palaeopathology articles in the International Journal of Paleopathology during the first ten years of publication (2011-2020), and to compare these results with those from other similar journals.

METHODS

The method used is bibliometry of International Journal of Paleopathology plus nine other periodicals publishing in the field of osteoarchaeology / palaeopathology. In these ten journals, 2513 publications in human osteology are reviewed of which 1032 are devoted specifically or substantially to palaeopathology.

RESULTS

International Journal of Paleopathology has attracted a large number of palaeopathology publications, but this has not been at the expense of extant journals. Its appearance appears to have coincided with an expansion of the discipline, and it may also act as a focus for publication for articles that would not previously have found a venue. Its output is distinctive from other journals assessed, with greater emphasis on review articles (including those focusing on method and theory in palaeopathology) and, especially, on case reports.

SIGNIFICANCE

International Journal of Paleopathology acts as a focal point for publications from diverse areas of the field. The connection with the Paleopathology Association provides a conduit by which outcomes of debates within the profession concerning future priorities for the field (e.g. development of method and theory; the status of the case report within the discipline) can be reflected in journal policy.

LIMITATIONS

Palaeopathology and other osteoarchaeology articles are published in venues other than those analysed in the current work.

Archaeogenetics: What Can Ancient Genomes Tell Us about the Origin of Syphilis?

The origin of syphilis has been hotly debated for decades. Ancient pathogen DNA may provide new evidence to redefine our understanding of this mystery, but is the mystery itself flawed in its assumptions?

Human major infections: Tuberculosis, treponematoses, leprosy-A paleopathological perspective of their evolution

The key to evolution is reproduction. Pathogens can either kill the human host or can invade the host without causing death, thus ensuring their own survival, reproduction and spread. Tuberculosis, treponematoses and leprosy are widespread chronic infectious diseases whereby the host is not immediately killed. These diseases are examples of the co-evolution of host and pathogen. They can be well studied as the paleopathological record is extensive, spanning over 200 human generations. The paleopathology of each disease has been well documented in the form of published synthetic analyses recording each known case and case frequencies in the samples they were derived from. Here the data from these synthetic analyses were re-analysed to show changes in the prevalence of each disease over time. A total of 69,379 skeletons are included in this study. There was ultimately a decline in the prevalence of each disease over time, this decline was statistically significant (Chi-squared, p<0.001). A trend may start with the increase in the disease’s prevalence before the prevalence declines, in tuberculosis the decline is monotonic. Increase in skeletal changes resulting from the respective diseases appears in the initial period of host-disease contact, followed by a decline resulting from co-adaptation that is mutually beneficial for the disease (spread and maintenance of pathogen) and host (less pathological reactions to the infection). Eventually either the host may become immune or tolerant, or the pathogen tends to be commensalic rather than parasitic.

Syphilis in an Italian medieval jewish community: A bioarchaeological and cultural perspective

OBJECTIVES

We aim to discuss the presence of treponemal infections in three individuals belonging to a large (∼400 individuals) Late Medieval cemetery (14th -16th century) that archaeological and documentary sources place within a Jewish context, and to discuss the role of these diseases in a biocultural perspective.

MATERIALS AND METHODS

An anthropological and paleopathological study was conducted on skeletal remains of three individuals, though macroscopic and tomographic examination.

RESULTS

Cranial lesions in which simultaneous destructive and proliferative processes (caries sicca) are noted. Long bones also present osseous alterations with increased bone density and non-uniform thickening.

CONCLUSIONS

Skeletal lesions are consistent with treponemal infections (possibly either endemic or acquired syphilis). Historical documentation could help the interpretation of our cases, recording a syphilis outbreak in Bologna in 1496, possibly coeval to the Late Medieval Jewish cemetery.

SIGNIFICANCE

These cases of treponematosis are unique, documenting the presence of the disease within the Jewish Medieval community in Italy, as they frame the effects and consequence of the infection in shaping social and cultural contexts of the medieval Italian and European communities. They offer material evidence to elaborate on the historical documents on the hostility Jewish community suffered.

LIMITATIONS

Radiocarbon dating have not been performed directly on skeletal remains of the three pathological individuals. δ¹³C and δ¹⁵N isotope ratios should also be acquired to estimate the marine diet component, to account for possible marine reservoir effect on radiocarbon age calibration.

A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe

Developments in techniques for identification of pathogen DNA in archaeological samples can expand our resolution of disease detection. Our application of a non-targeted molecular screening tool for the parallel detection of pathogens in historical plague victims from post-medieval Lithuania revealed the presence of more than one active disease in one individual. In addition to Yersinia pestis, we detected and genomically characterized a septic infection of Treponema pallidum pertenue, a subtype of the treponemal disease family recognised as the cause of the tropical disease yaws. Our finding in northern Europe of a disease that is currently restricted to equatorial regions is interpreted within an historical framework of intercontinental trade and potential disease movements. Through this we offer an alternative hypothesis for the history and evolution of the treponemal diseases, and posit that yaws be considered an important contributor to the sudden epidemic of late 15^th century Europe that is widely ascribed to syphilis.

The Immune System and Responses to Cancer: Coordinated Evolution

This review explores the incessant evolutionary interaction and co-development between immune system evolution and somatic evolution, to put it into context with the short, over 60-year, detailed human study of this extraordinary protective system. Over millions of years, the evolutionary development of the immune system in most species has been continuously shaped by environmental interactions between microbes, and aberrant somatic cells, including malignant cells. Not only has evolution occurred in somatic cells to adapt to environmental pressures for survival purposes, but the immune system and its function has been successively shaped by those same evolving somatic cells and microorganisms through continuous adaptive symbiotic processes of progressive simultaneous immunological and somatic change to provide what we observe today. Indeed, the immune system as an environmental influence has also shaped somatic and microbial evolution. Although the immune system is tuned to primarily controlling microbiological challenges for combatting infection, it can also remove damaged and aberrant cells, including cancer cells to induce long-term cures. Our knowledge of how this occurs is just emerging. Here we consider the connections between immunity, infection and cancer, by searching back in time hundreds of millions of years to when multi-cellular organisms first began. We are gradually appreciating that the immune system has evolved into a truly brilliant and efficient protective mechanism, the importance of which we are just beginning to now comprehend. Understanding these aspects will likely lead to more effective cancer and other therapies.