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dc.contributor.authorBeale, Mathew A
dc.contributor.authorMarks, Michael
dc.contributor.authorCole, Michelle J
dc.contributor.authorLee, Min-Kuang
dc.contributor.authorPitt, Rachel
dc.contributor.authorRuis, Christopher
dc.contributor.authorBalla, Eszter
dc.contributor.authorCrucitti, Tania
dc.contributor.authorEwens, Michael
dc.contributor.authorFernández-Naval, Candela
dc.contributor.authorGrankvist, Anna
dc.contributor.authorGuiver, Malcolm
dc.contributor.authorKenyon, Chris R
dc.contributor.authorKhairullin, Rafil
dc.contributor.authorKularatne, Ranmini
dc.contributor.authorArando, Maider
dc.contributor.authorMolini, Barbara J
dc.contributor.authorObukhov, Andrey
dc.contributor.authorPage, Emma E
dc.contributor.authorPetrovay, Fruzsina
dc.contributor.authorRietmeijer, Cornelis
dc.contributor.authorRowley, Dominic
dc.contributor.authorShokoples, Sandy
dc.contributor.authorSmit, Erasmus
dc.contributor.authorSweeney, Emma L
dc.contributor.authorTaiaroa, George
dc.contributor.authorVera, Jaime H
dc.contributor.authorWennerås, Christine
dc.contributor.authorWhiley, David M
dc.contributor.authorWilliamson, Deborah A
dc.contributor.authorHughes, Gwenda
dc.contributor.authorNaidu, Prenilla
dc.contributor.authorUnemo, Magnus
dc.contributor.authorKrajden, Mel
dc.contributor.authorLukehart, Sheila A
dc.contributor.authorMorshed, Muhammad G
dc.contributor.authorFifer, Helen
dc.contributor.authorThomson, Nicholas R
dc.descriptionFunder: Queensland Government
dc.description.abstractSyphilis, 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.
dc.publisherSpringer Science and Business Media LLC
dc.rightsAttribution 4.0 International
dc.sourceessn: 2058-5276
dc.sourcenlmid: 101674869
dc.subjectTreponema pallidum
dc.subjectAnti-Bacterial Agents
dc.subjectDrug Resistance, Bacterial
dc.subjectGenome, Bacterial
dc.titleGlobal phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.
prism.publicationNameNat Microbiol
dc.contributor.orcidBeale, Mathew A [0000-0002-4740-3187]
dc.contributor.orcidMarks, Michael [0000-0002-7585-4743]
dc.contributor.orcidLee, Min-Kuang [0000-0002-0205-9482]
dc.contributor.orcidRuis, Christopher [0000-0003-0977-5534]
dc.contributor.orcidBalla, Eszter [0000-0001-8519-9511]
dc.contributor.orcidFernández-Naval, Candela [0000-0002-5584-3537]
dc.contributor.orcidKhairullin, Rafil [0000-0001-9879-378X]
dc.contributor.orcidObukhov, Andrey [0000-0001-6320-9651]
dc.contributor.orcidSmit, Erasmus [0000-0003-3286-798X]
dc.contributor.orcidVera, Jaime H [0000-0002-1165-0573]
dc.contributor.orcidWilliamson, Deborah A [0000-0001-7363-6665]
dc.contributor.orcidNaidu, Prenilla [0000-0002-7028-098X]
dc.contributor.orcidLukehart, Sheila A [0000-0001-9778-3301]
dc.contributor.orcidThomson, Nicholas R [0000-0002-4432-8505]
pubs.funder-project-idNIAID NIH HHS (R01 AI042143, R01 AI123196)
pubs.funder-project-idMedical Research Council (MR/V027956/1)
pubs.funder-project-idU.S. Department of Health &amp (R01 AI123196, R01 AI42143)
pubs.funder-project-idDepartment of Health | National Health and Medical Research Council (1174555)
pubs.funder-project-idWellcome Trust (206194)
pubs.funder-project-idDH | NIHR | Programme Development Grants (NIHR200125)
pubs.funder-project-idNational Institute for Health Research (NIHR) (NIHR200125)
pubs.funder-project-idEuropean and Developing Countries Clinical Trials Partnership (RIA2018D-249)

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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International