Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages

Mathew A. Beale (), Michael Marks, Sharon K. Sahi, Lauren C. Tantalo, Achyuta V. Nori, Patrick French, Sheila A. Lukehart, Christina M. Marra and Nicholas R. Thomson ()
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Mathew A. Beale: Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus
Michael Marks: London School of Hygiene & Tropical Medicine
Sharon K. Sahi: University of Washington
Lauren C. Tantalo: University of Washington
Achyuta V. Nori: Guy’s & St Thomas’ NHS Foundation Trust
Patrick French: The Mortimer Market Centre CNWL, Camden Provider Services
Sheila A. Lukehart: University of Washington
Christina M. Marra: University of Washington
Nicholas R. Thomson: Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus

Nature Communications, 2019, vol. 10, issue 1, 1-9

Abstract: Abstract Syphilis is a sexually transmitted infection caused by Treponema pallidum subspecies pallidum and may lead to severe complications. Recent years have seen striking increases in syphilis in many countries. Previous analyses have suggested one lineage of syphilis, SS14, may have expanded recently, indicating emergence of a single pandemic azithromycin-resistant cluster. Here we use direct sequencing of T. pallidum combined with phylogenomic analyses to show that both SS14- and Nichols-lineages are simultaneously circulating in clinically relevant populations in multiple countries. We correlate the appearance of genotypic macrolide resistance with multiple independently evolved SS14 sub-lineages and show that genotypically resistant and sensitive sub-lineages are spreading contemporaneously. These findings inform our understanding of the current syphilis epidemic by demonstrating how macrolide resistance evolves in Treponema subspecies and provide a warning on broader issues of antimicrobial resistance.

Date: 2019
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DOI: 10.1038/s41467-019-11216-7

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