Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia: a genomic epidemiological analysis

ML Taouk; G Taiaroa; S Pasricha; S Herman; EPF Chow; F Azzatto; B Zhang; CM Sia; S Duchene; A Lee; N Higgins; J Prestedge; YW Lee; NR Thomson; B Graves; E Meumann; M Gunathilake; JS Hocking; CS Bradshaw; MA Beale; BP Howden; MY Chen; CK Fairley; DJ Ingle; DA Williamson

Journal article

Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia: a genomic epidemiological analysis

ML Taouk, G Taiaroa, S Pasricha, S Herman, EPF Chow, F Azzatto, B Zhang, CM Sia, S Duchene, A Lee, N Higgins, J Prestedge, YW Lee, NR Thomson, B Graves, E Meumann, M Gunathilake, JS Hocking, CS Bradshaw, MA Beale Show all

Lancet Microbe | Published : 2022

DOI: 10.1016/S2666-5247(22)00035-0

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Abstract

Background: The incidence of syphilis has increased markedly in the past decade in high-income countries, including Australia. To date, however, genomic studies of Treponema pallidum have focused mainly on the northern hemisphere. Here, we aimed to characterise the lineages of T pallidum driving the current syphilis epidemic in Australia. Methods: In this genomic epidemiological analysis, using phylogenomic and phylodynamic analyses, we analysed 456 high-quality T pallidum genomes collected from clinical samples in Australia between Oct 19, 2005, and Dec 31, 2020, and contextualised this information with publicly available sequence data. We also performed detailed genomic characterisation of..

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University of Melbourne Researchers

George Taiaroa Author

Shivani Pasricha Author

Eric Chow Author

Sebastian Duchene Garzon Author

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Awarded by Wellcome Trust

Funding Acknowledgements

This study was funded by the National Health and Medical Research Council Australia (NHMRC; GNT1147735). SD was funded by the Australian Research Council (DE190100805). NRT and MAB were funded by the Wellcome Trust (grant 206194). CKF is supported by an NHMRC Investigator Grant (APP1172900). DJI is supported by an NHMRC Investigator Grant (APP1195210). DAW is supported by an NHMRC Investigator Grant (APP1174555). Part of this research was undertaken using the Linkage Infrastructure, Equipment and Facilities high performance computer General-Purpose Graphics Processing Unit Facility hosted at the University of Melbourne. This facility was established with the assistance of LIEF Grant LE170100200. We gratefully acknowledge Shellee Williams from the Northern Territory Centre for Disease Control for assistance with identifying syphilis cases, and Kevin Freeman from Territory Pathology for assistance identifying pathology specimens for inclusion in the study.