TY - JOUR
T1 - Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia
T2 - a genomic epidemiological analysis
AU - Taouk, Mona L
AU - Taiaroa, George
AU - Pasricha, Shivani
AU - Herman, Sophie
AU - Chow, Eric P F
AU - Azzatto, Francesca
AU - Zhang, Bowen
AU - Sia, Cheryll M
AU - Duchene, Sebastian
AU - Lee, Alvin
AU - Higgins, Nasra
AU - Prestedge, Jacqueline
AU - Lee, Yi Wei
AU - Thomson, Nicholas R
AU - Graves, Bianca
AU - Meumann, Ella
AU - Gunathilake, Manoji
AU - Hocking, Jane S
AU - Bradshaw, Catriona S
AU - Beale, Mathew A
AU - Howden, Benjamin P
AU - Chen, Marcus Y
AU - Fairley, Christopher K
AU - Ingle, Danielle J
AU - Williamson, Deborah A
N1 - Copyright © 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 license. Published by Elsevier Ltd.. All rights reserved.
PY - 2022/6/1
Y1 - 2022/6/1
N2 - 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 putative antimicrobial resistance determinants, in addition to correlating single-locus typing of the TP0548 allele with the T pallidum phylogeny.FINDINGS: Phylogenomic analyses identified four major sublineages circulating in Australia and globally, two belonging to the SS14 lineage, and two belonging to the Nichols lineage. Australian sublineages were further delineated into twelve subgroups, with five of the six largest subgroups associated with men who have sex with men, and the sixth lineage was predominantly associated with heterosexual people. Most Australian T pallidum genomes (398 [87%] of 456) were genotypically macrolide resistant, and TP0548 typing correlated significantly with T pallidum genomic subgroups.INTERPRETATION: These findings show that the current syphilis epidemic in Australia is driven by multiple lineages of T pallidum, rather than one distinct outbreak. Major subgroups of T pallidum in Australia have emerged within the past 30 years, are closely related to global lineages, and circulate across different sexual networks. In conjunction with improved testing and treatment, these data could better inform the control of syphilis in Australia.FUNDING: National Health and Medical Research Council, Australian Research Council.
AB - 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 putative antimicrobial resistance determinants, in addition to correlating single-locus typing of the TP0548 allele with the T pallidum phylogeny.FINDINGS: Phylogenomic analyses identified four major sublineages circulating in Australia and globally, two belonging to the SS14 lineage, and two belonging to the Nichols lineage. Australian sublineages were further delineated into twelve subgroups, with five of the six largest subgroups associated with men who have sex with men, and the sixth lineage was predominantly associated with heterosexual people. Most Australian T pallidum genomes (398 [87%] of 456) were genotypically macrolide resistant, and TP0548 typing correlated significantly with T pallidum genomic subgroups.INTERPRETATION: These findings show that the current syphilis epidemic in Australia is driven by multiple lineages of T pallidum, rather than one distinct outbreak. Major subgroups of T pallidum in Australia have emerged within the past 30 years, are closely related to global lineages, and circulate across different sexual networks. In conjunction with improved testing and treatment, these data could better inform the control of syphilis in Australia.FUNDING: National Health and Medical Research Council, Australian Research Council.
KW - Anti-Bacterial Agents
KW - Australia/epidemiology
KW - Disease Outbreaks
KW - Genomics
KW - Homosexuality, Male
KW - Humans
KW - Male
KW - Sexual and Gender Minorities
KW - Syphilis/epidemiology
KW - Treponema pallidum/genetics
U2 - 10.1016/S2666-5247(22)00035-0
DO - 10.1016/S2666-5247(22)00035-0
M3 - Article
C2 - 35659903
SN - 2666-5247
VL - 3
SP - e417-e426
JO - The Lancet Microbe
JF - The Lancet Microbe
IS - 6
ER -