Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue

Abstract

BackgroundIncreasing evidence suggests many non-human primate (NHP) species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue (TPE), the bacterium causing yaws in humans. In humans, yaws is characterized by lesions of the extremities and face, while Treponema pallidum subsp. pallidum (TPA) causes venereal syphilis and is characterized by primary lesions on the genital, anal or oral mucosae, and has not been detected in NHPs. Due to a paucity of genetic data, it remains unclear whether other Treponema pallidum (TP) subspecies found in humans also occur in NHP and how the genomic diversity of TPE lineages that do occur in NHPs is distributed across hosts and space. MethodologyWe observed a combination of yaws-and syphilis-like symptoms in sooty mangabeys (Cercocebus atys atys) in Taï National Park (TNP), Côte d'Ivoire and collected swabs and biopsies from symptomatic animals. We also collected NHP bones from eight species from TNP, as well as from 19 species at 12 field sites across sub-Saharan Africa. Samples were screened for TP DNA using PCRs. In-solution hybridization capture coupled with high throughput sequencing was used to sequence TP genomes from positive samples. Principal findingsWe generated four nearly complete TP genomes from biopsies and swabs and five partial genomes from bones. Phylogenomic analyses revealed that both syphilis-and yaws-like lesions of sooty mangabeys within a single social group in TNP were caused by TPE. All TPE genomes determined from these sooty mangabeys were different and exhibited divergence levels not observed in TPE from a single species at any other field site where the disease seems to be epizootic. In general, simian TPE isolates did not form monophyletic clades based on host species or the type of symptoms caused by an isolate, but rather clustered based on geography. ConclusionsThere is a large diversity of TPE strains infecting NHPs in TNP. Our observations within a single social group of sooty mangabeys do not support the epizootic spread of a single clone, but rather points towards frequent independent introductions of the bacterium, which can cause syphilis-and yaws-like lesions. On a larger scale, the geographic clustering of TPE genomes might be compatible with cross-species transmission of TPE within ecosystems or environmental exposure leading to acquisition of closely related strains. Author's summaryIndividuals in several populations of wild non-human primates (NHP) in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue (TPE), a pathogen causing yaws disease in humans. In humans, yaws is characterized by skin lesions of the extremities and face. In contrast, Treponema pallidum subsp. pallidum, which causes venereal syphilis in humans, has not been observed in NHPs. We describe a combination of yaws-and syphilislike symptoms in a sooty mangabey (Cercocebus atys atys) social group in Taï National Park (TNP), Côte d'Ivoire. We sampled lesioned animals and collected and tested NHP bones from field sites across sub-Saha...

Epidemiologic and Genomic Reidentification of Yaws, Liberia

“…These human-derived TPE genomes appearing completely unrelated to those from nonhuman primates, coupled with our detection of only a single monophyletic clade, highlight the importance of geography on TPE population structure. This finding is also inconsistent with recent zoonotic transmission between humans and the nonhuman primates in this area ( 17 ), although more intensive, localized sampling is needed to affirm our understanding of TPE as a potential zoonosis.…”

“…Despite their close genetic relationship, few whole-genome sequences are currently available for TPE. Furthermore, yaws-like disease caused by TPE has now been detected in nonhuman primate species in several countries in sub-Saharan Africa, including Côte d’Ivoire ( 16 , 17 ). The direct role of nonhuman primate species as a potential reservoir for zoonotic infection is currently unknown, but it may prove critical to guiding eradication strategies ( 16 ).…”