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Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis
Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK; Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, UK.
HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK.
British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada.
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2021 (English)In: Nature Microbiology, E-ISSN 2058-5276, Vol. 6, no 12, p. 1549-1560Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Nature Publishing Group, 2021. Vol. 6, no 12, p. 1549-1560
National Category
Infectious Medicine
Identifiers
URN: urn:nbn:se:oru:diva-95586DOI: 10.1038/s41564-021-01000-zISI: 000722274600015PubMedID: 34819643Scopus ID: 2-s2.0-85119854843OAI: oai:DiVA.org:oru-95586DiVA, id: diva2:1614665
Funder
Wellcome trust, 206194
Note

Funding agencies:

National Health and Medical Research Council of Australia 1174555  

United States Department of Health & Human Services

National Institutes of Health (NIH) - USA

NIH National Institute of Allergy & Infectious Diseases (NIAID) R01 AI123196  

UK Research & Innovation (UKRI)

Medical Research Council UK (MRC) MR/V027956/1  

United States Department of Health & Human Services

National Institutes of Health (NIH) - USA R01 AI42143

DH | NIHR | Programme Development Grants (NIHR Programme Development Grants) NIHR200125  

European and Developing Countries Clinical Trials Partnership (EDCTP) RIA2018D-249

Available from: 2021-11-26 Created: 2021-11-26 Last updated: 2023-12-08Bibliographically approved

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