在澳大利亚当代梅毒疫情中苍白密螺旋体谱系的特征：基因组流行病学分析。

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

机构信息

Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia; Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia; Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia.

出版信息

Lancet Microbe. 2022 Jun;3(6):e417-e426. doi: 10.1016/S2666-5247(22)00035-0. Epub 2022 Apr 20.

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

PMID:35659903

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 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.

摘要

背景

梅毒发病率在过去十年中在包括澳大利亚在内的高收入国家显著上升。然而，迄今为止，苍白密螺旋体的基因组研究主要集中在北半球。在这里，我们旨在描述导致当前澳大利亚梅毒流行的苍白密螺旋体谱系。

方法

在这项基因组流行病学分析中，我们使用系统发育基因组学和系统发育动力学分析，分析了 2005 年 10 月 19 日至 2020 年 12 月 31 日期间从澳大利亚临床样本中收集的 456 株高质量苍白密螺旋体基因组，并将这些信息与公开可用的序列数据进行了关联。我们还对假定的抗生素耐药决定因素进行了详细的基因组特征分析，此外还将 TP0548 等位基因的单基因座分型与苍白密螺旋体系统发育相关联。

结果

系统发育基因组分析确定了在澳大利亚和全球流行的四个主要亚谱系，其中两个属于 SS14 谱系，两个属于 Nichols 谱系。澳大利亚亚谱系进一步细分为十二个亚群，其中六个最大亚群中的五个与男男性行为者相关，第六个谱系主要与异性恋者相关。大多数澳大利亚苍白密螺旋体基因组（456 个中的 398 个，占 87%）在基因型上对大环内酯类耐药，TP0548 分型与苍白密螺旋体基因组亚群显著相关。