Abstract:Sexually transmitted (venereal) syphilis marked European history with a devastating epidemic at the end of the 15 th century, and is currently re-emerging globally. Together with non-venereal treponemal diseases, like bejel and yaws, found in subtropical and tropical regions, it poses a prevailing health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeo… Show more
“…The oldest bone from which we were able to phylogenetically assign reads to the TPE clade was collected in 1992, complementing clinical evidence from TNP that only started accumulating from 2014 onward [12]. Our results suggest that, together with archaeological collections [67–69], natural history specimens can provide important genomic information regarding TPE and thereby further our understanding of its ecology and evolution.…”
Many non-human primate species in sub-Saharan Africa are infected with
Treponema pallidum
subsp.
pertenue
, the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while
T. pallidum
subsp.
pallidum
causes venereal syphilis and is typically characterized by primary lesions on the genital, anal or oral mucosae. It remains unclear whether other
T. pallidum
subspecies found in humans also occur in non-human primates and how the genomic diversity of non-human primate
T. pallidum
subsp.
pertenue
lineages is distributed across hosts and space. We observed orofacial and genital lesions in sooty mangabeys (Cercocebus atys) in Taï National Park, Côte d’Ivoire and collected swabs and biopsies from symptomatic animals. We also collected non-human primate bones from 8 species in Taï National Park and 16 species from 11 other sites across sub-Saharan Africa. Samples were screened for
T. pallidum
DNA using polymerase chain reactions (PCRs) and we used in-solution hybridization capture to sequence
T. pallidum
genomes. We generated three nearly complete
T. pallidum
genomes from biopsies and swabs and detected treponemal DNA in bones of six non-human primate species in five countries, allowing us to reconstruct three partial genomes. Phylogenomic analyses revealed that both orofacial and genital lesions in sooty mangabeys from Taï National Park were caused by
T. pallidum
subsp.
pertenue
. We showed that
T. pallidum
subsp.
pertenue
has infected non-human primates in Taï National Park for at least 28 years and has been present in two non-human primate species that had not been described as
T. pallidum
subsp.
pertenue
hosts in this ecosystem, western chimpanzees (Pan troglodytes verus) and western red colobus (Piliocolobus badius), complementing clinical evidence that started accumulating in Taï National Park in 2014. More broadly, simian
T. pallidum
subsp.
pertenue
strains did not form monophyletic clades based on host species or the symptoms caused, but rather clustered based on geography. Geographical clustering of
T. pallidum
subsp.
pertenue
genomes might be compatible with cross-species transmission of
T. pallidum
subsp.
pertenue
within ecosystems or environmental exposure, leading to the acquisition of closely related strains. Finally, we found no evidence for mutations that confer antimicrobial resistance.
“…The oldest bone from which we were able to phylogenetically assign reads to the TPE clade was collected in 1992, complementing clinical evidence from TNP that only started accumulating from 2014 onward [12]. Our results suggest that, together with archaeological collections [67–69], natural history specimens can provide important genomic information regarding TPE and thereby further our understanding of its ecology and evolution.…”
Many non-human primate species in sub-Saharan Africa are infected with
Treponema pallidum
subsp.
pertenue
, the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while
T. pallidum
subsp.
pallidum
causes venereal syphilis and is typically characterized by primary lesions on the genital, anal or oral mucosae. It remains unclear whether other
T. pallidum
subspecies found in humans also occur in non-human primates and how the genomic diversity of non-human primate
T. pallidum
subsp.
pertenue
lineages is distributed across hosts and space. We observed orofacial and genital lesions in sooty mangabeys (Cercocebus atys) in Taï National Park, Côte d’Ivoire and collected swabs and biopsies from symptomatic animals. We also collected non-human primate bones from 8 species in Taï National Park and 16 species from 11 other sites across sub-Saharan Africa. Samples were screened for
T. pallidum
DNA using polymerase chain reactions (PCRs) and we used in-solution hybridization capture to sequence
T. pallidum
genomes. We generated three nearly complete
T. pallidum
genomes from biopsies and swabs and detected treponemal DNA in bones of six non-human primate species in five countries, allowing us to reconstruct three partial genomes. Phylogenomic analyses revealed that both orofacial and genital lesions in sooty mangabeys from Taï National Park were caused by
T. pallidum
subsp.
pertenue
. We showed that
T. pallidum
subsp.
pertenue
has infected non-human primates in Taï National Park for at least 28 years and has been present in two non-human primate species that had not been described as
T. pallidum
subsp.
pertenue
hosts in this ecosystem, western chimpanzees (Pan troglodytes verus) and western red colobus (Piliocolobus badius), complementing clinical evidence that started accumulating in Taï National Park in 2014. More broadly, simian
T. pallidum
subsp.
pertenue
strains did not form monophyletic clades based on host species or the symptoms caused, but rather clustered based on geography. Geographical clustering of
T. pallidum
subsp.
pertenue
genomes might be compatible with cross-species transmission of
T. pallidum
subsp.
pertenue
within ecosystems or environmental exposure, leading to the acquisition of closely related strains. Finally, we found no evidence for mutations that confer antimicrobial resistance.
“…For example, this genomic-scale work has led to revised narratives on the temporal-spatial emergence and transmission of M. tuberculosis and M. leprae , generated indisputable evidence of the bacterium responsible for yaws ( Treponema palladium pertenue ) being present in Western Europe before the journeys of Columbus and revealed the global dispersal of ubiquitous human pathogens, including hepatitis B virus ( Box 1 ) and Helicobacter pylori . In combination, this work will continue to revise our understanding of the history of infectious disease [ 4 , 13 , 14 , 15 ]. Genetics does not meet history: Hepatitis B virus.…”
Section: Main Textmentioning
confidence: 99%
“…Treponema pallidum pallidum and pertenue (causative agents of syphilis and yaws, respectively) sit at the other end of the spectrum because they lack an outer cell membrane altogether. This feature, coupled with the low pathogenic load of Treponema in late stages of infection [ 45 ], largely precluded its identification in ancient remains [ 45 , 46 , 47 ] until the recent application of high-throughput sequencing methods [ 15 , 17 , 48 ].…”
The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest-premodern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae)-and for three equally important endemic human disease agents-Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20 th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.
“…Additionally, several biomolecular studies focused on diet and nutrition in ancient Estonian populations (Lõugas et al, 1996;Allmäe et al, 2012;Tõrv & Meadows, 2015;Lightfoot et al, 2016;Oras et al, 2018;Aguraiuja-Lätti & Lõugas, 2019;Tõrv, 2019). Specific paleopathological investigations were dedicated to cases of traumatic injuries (Kalman, 2000a(Kalman, , 2000b(Kalman, , 2000cMalve, 2019aMalve, , 2019bMalve, , 2020a, inflammatory lesions (Kalman, 1999), syphilis (Kalman, 2000d;; and the biomolecular study by Majander et al, 2020), infectious disease (Malve, 2020b) oral pathologies (Allmäe, 1999a(Allmäe, , 1999bLimbo, 2004Limbo, , 2011Limbo, , 2013, and stress markers (Limbo, 2006(Limbo, , 2008a(Limbo, , 2008b(Limbo, , 2009Allmäe & Limbo, 2010).…”
The skeletal remains of non-adults provide endless insights into numerous aspects of their personal, family and social lives. Although they were considered to be marginal members of society, children can potentially shed light on factors influencing the overall health and survival of their communities, sensitively conveying the ability of a population to adapt to its environment and cope with moments of crisis. In the last decade, worldwide interest in the archaeology of children has grown, and has driven the bioarchaeological investigation of their skeletal remains. However, the bioarchaeological study of non-adults has received surprisingly little interest in the Baltic states. This review presents the past and current state of the art with specific focus on the Baltic area from prehistory to historic times, outlining new research fields and the benefits of studying non-adult skeletal remains, and proposing specific possible directions for future work on this topic. The paper is aimed at giving a louder voice to the youngest actors of ancient communities, and perhaps offers a starting point for developing a definitive bioarchaeology of children in the Baltics.
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