Analysis of <i>Treponema pallidum</i> Strains From China Using Improved Methods for Whole-Genome Sequencing From Primary Syphilis Chancres

Chen, Wentao; Šmajs, David; Hu, Yongfei; Ke, Wujian; Pospíšilová, Petra; Hawley, Kelly L.; Caimano, Melissa J.; Radolf, Justin D.; Seña, Arlene C.; Tucker, Joseph D.; Yang, Bin; Juliano, Jonathan J.; Zheng, Heping; Parr, Jonathan B.

doi:10.1093/infdis/jiaa449

Cited by 20 publications

(26 citation statements)

References 15 publications

(20 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We performed targeted sequence-capture whole genome sequencing on residual genomic DNA extracted from diagnostic swabs taken from TPA PCR positive syphilis patients, and on TPA strains previously isolated in rabbits. We combined these data with 133 previously published genomes 3,4,17–19,22–25 . After assessment for genome coverage and quality, we had a total of 726 genomes with >25% of genome positions at >5X coverage (mean 82%, range 25-97%), sufficient for primary lineage classification.…”

Section: Resultsmentioning

confidence: 99%

“…Our understanding of Nichols-lineage is predominantly limited to laboratory strains from the USA, with relatively few clinical strains sequenced 4,16 . However, most TPA genomes published to date originate from the USA 4 , Western Europe 3,4,16,17 and China 18,19 , and our understanding of the true breadth of diversity of TPA is incomplete 20 . This is partly explained, by the fact it has not been possible to culture TPA outside of a rabbit until recently 21 , and also explains why our view of the diversity of syphilis samples predating the 21 st century is even more limited.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Contemporary syphilis is characterised by rapid global spread of pandemicTreponema pallidumlineages

Beale

Marks

Cole

et al. 2021

Preprint

View full text Add to dashboard Cite

Syphilis is an important sexually transmitted infection caused by the bacterium Treponema pallidum subspecies pallidum. The last two decades have seen syphilis incidence rise in many high-income countries, yet the evolutionary and epidemiological relationships that underpin this are poorly understood, as is the global T. pallidum population structure. We assembled a geographically and temporally diverse collection of clinical and laboratory samples comprising 726 T. pallidum genomes. We used detailed phylogenetic analysis and clustering to show that syphilis globally can be described by only two deeply branching lineages, Nichols and SS14. We show that both of these lineages can be found circulating concurrently in 12 of the 23 countries sampled. To provide further phylodynamic resolution we subdivided Treponema pallidum subspecies pallidum into 17 distinct sublineages. Importantly, like SS14, we provide evidence that two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analysis showed that recent isolates circulating in 14 different countries were genetically identical in their core genome to those from other countries, suggesting frequent exchange through international transmission pathways. This contrasts with the majority of samples collected prior to 1983, which are phylogenetically distinct from these more recently isolated sublineages. Bayesian temporal analysis provided evidence of a population bottleneck and decline occurring during the late 1990s, followed by a rapid population expansion a decade later. This was driven by the dominant T. pallidum sublineages circulating today, many of which are resistant to macrolides. Combined we show that the population of contemporary syphilis in high-income countries has undergone a recent and rapid global expansion.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Contemporary syphilis is characterised by rapid global spread of pandemicTreponema pallidumlineages

Beale

Marks

Cole

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Our understanding of the Nichols lineage is predominantly limited to laboratory strains from the USA, with relatively few clinical strains sequenced 4,17 . However, most TPA genomes published to date originate from the USA 4 , Western Europe 3,4,17,18 and China 19,20 , and our understanding of the true breadth of diversity of TPA is incomplete 21 . Our view of the diversity of syphilis samples pre-dating the…”

mentioning

confidence: 99%

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

Beale

Marks

Cole³

et al. 2021

Nat Microbiol

View full text Add to dashboard Cite

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.

show abstract

“…These have identified some epidemiological features related to the subtype and to the prevalence of macrolide resistance in strains in different countries 6 . Although whole-genome sequence (WGS) analyses have provided phylogenetic information on TPA strains in several countries [7][8][9][10][11][12][13][14] , those data have not necessarily been accumulated enough for comprehension of the overall aspects of the TPA circulations in the world.…”

mentioning

confidence: 99%

Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

Nishiki

Lee

Kanai

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Japan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.

show abstract

Analysis of Treponema pallidum Strains From China Using Improved Methods for Whole-Genome Sequencing From Primary Syphilis Chancres

Cited by 20 publications

References 15 publications

Contemporary syphilis is characterised by rapid global spread of pandemicTreponema pallidumlineages

Contemporary syphilis is characterised by rapid global spread of pandemicTreponema pallidumlineages

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

Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

Contact Info

Product

Resources

About