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

Abstract

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.

Serum Interleukin-26 is a Potential Biomarker for the Differential Diagnosis of Neurosyphilis and Syphilis at Other Stages

“…Syphilis is a globally prevalent multisystemic and chronic infection caused by the spirochetal bacterium Treponema pallidum subspecies pallidum ( T. pallidum ). 1 It can be transmitted through blood transfusion and derivatives, unprotected sexual intercourse and maternal-neonatal transmission. Syphilis is still a major public health problem, with estimated 36 million occurrences and 12 million new cases worldwide.…”

Putting a twist in syphilis vaccine development

“…Genome sequencing revealed that two major TPA lineages, Nichols and SS14, co-circulate across multiple continents. The genetically homogeneous SS14 lineage was the dominant lineage in most sampled regions; however, both lineages exhibited similar phylodynamics and are responsible for current epidemics 1 – 3 . Furthermore, TPA populations circulating among patients in the twentieth century may have been different from the modern populations 1 , 3 .…”

“…The genetically homogeneous SS14 lineage was the dominant lineage in most sampled regions; however, both lineages exhibited similar phylodynamics and are responsible for current epidemics 1 – 3 . Furthermore, TPA populations circulating among patients in the twentieth century may have been different from the modern populations 1 , 3 . This has been linked to a population bottleneck in the late 1990s, followed by the expansion of modern sublineages in the 2000s.…”

“…Hybridization capture using DNA or RNA probes designed based on TPA genomes has become the most popular and efficient technique for this targeted genome sequencing. Three recently published studies used this technology for large-scale sequencing of TPA, which enabled the deep exploration of modern syphilis epidemics 1 – 3 .…”

Relato de caso: alterações ósseas de sífilis congênita refratária ao tratamento em escolar de 7 anos

“…Chama atenção a repetição de casos em uma mesma família. Para caracterizar a estrutura populacional global de T. pallidum,Beale et al, 2021 sequenciaram amostras de 23 países em todo o mundo e analisaram as sequências do genoma e concluíram que todos os 726 genomas pertenciam a apenas duas linhagens, Nichols e SS14, com o último dominando e ambos circulando globalmente(Aoroa, 2016;Beale, 2019; Beale et al,2021).…”