Syphilis, caused by Treponema pallidum subsp. pallidum (TPA), remains an important public health problem with an increasing worldwide prevalence. Despite recent advances in in vitro cultivation, genetic variability of this pathogen during infection is poorly understood. Here, we present contemporary and geographically diverse complete treponemal genome sequences isolated directly from patients using a methyl-directed enrichment prior to sequencing. This approach reveals that approximately 50% of the genetic diversity found in TPA is driven by inter- and/or intra-strain recombination events, particularly in strains belonging to one of the defined genetic groups of syphilis treponemes: Nichols-like strains. Recombinant loci were found to encode putative outer-membrane proteins and the recombination variability was almost exclusively found in regions predicted to be at the host-pathogen interface. Genetic recombination has been considered to be a rare event in treponemes, yet our study unexpectedly showed that it occurs at a significant level and may have important impacts in the biology of this pathogen, especially as these events occur primarily in the outer membrane proteins. This study reveals the existence of strains with different repertoires of surface-exposed antigens circulating in the current human population, which should be taken into account during syphilis vaccine development.

Gonorrhea and chlamydia have increased among MSM despite the decrease in the number of sexual partners and are occurring primarily in MSM with high numbers of partners and persist after adjusting for known risk factors, suggesting that unmeasured factors (e.g., more assortative mixing patterns) may explain the observed changes.

BackgroundWe examined differences in incident HIV infection between newly-arrived Asian-born and other men who have sex with men (MSM) after the introduction of universal HIV treatment guidelines in 2015 and pre-exposure prophylaxis in 2016.MethodsClinical, demographic, laboratory and behavioural data on MSM presenting for HIV testing at the Melbourne Sexual Health Centre from July 2013 to June 2017 were extracted. We compared the proportion of newly-arrived (four years or less in Australia), Asian-born and other MSM tested each year who were diagnosed with incident HIV infection (negative test within one year or diagnosis with indeterminate or negative Western Blot).ResultsWe analysed 35,743 testing episodes in 12,180 MSM, including 2781 testing episodes in 1047 newly-arrived Asian-born MSM. The proportion of other MSM tested each year who were diagnosed with incident HIV infection fell from 0.83% in 2014 to 0.38% in 2017 (p = .001), but did not fall in newly-arrived Asian-born MSM (from 1.18% in 2014 to 1.56% in 2017, p = .76). In the multivariate logistic regression, in 2016/2017 but not in 2014/2015, being newly-arrived Asian-born was associated with an increased odds of diagnosis of incident HIV infection (aOR 3.29, 95%CI 1.82–5.94, p < .001).ConclusionsThe epidemiology of HIV in Melbourne Australia has changed dramatically. While there has been an overall reduction amongst MSM, the incidence of HIV in newly-arrived Asian-born MSM remains high. Failing to address these new inequalities leaves individuals at risk and may offset the population benefit of biomedical HIV prevention.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3325-0) contains supplementary material, which is available to authorized users.