Objectives We aimed to characterise patterns of anal and oral detection of Treponema pallidum among men who have sex with men (MSM) with early syphilis.

Methods 200 MSM with serologically confirmed primary, secondary and early latent syphilis were tested with T. pallidum polA PCR using an anal canal swab, oral rinse, plus swabs from any anal and oral lesions in a prospective, cross-sectional study. Anal and oral T. pallidum cycle threshold values were compared between subsets of men and according to rapid plasma reagin (RPR) titre.

Results Of 200 men with early syphilis, 45 and 48 had anal and oral T. pallidum detected, respectively. Cycle threshold values were lower with anal compared with oral T. pallidum whether lesions were present or not. Among 27 and 42 men with anal and oral T. pallidum detected, respectively, and no anal or oral primary lesion, frequency of detection increased with increasing RPR titre, with 95% (25/27) and 98% (41/42) of shedding from respective sites occurring with RPR titres ≥1:16. 6.5% (13/200) of men with syphilis had concurrent detection of T. pallidum from both anal and oral sites: 9/13 with secondary syphilis, 7/9 of whom had anal lesions with a median duration of 30 days (range 7–180 days).

Conclusions These data suggest T. pallidum load at the anus is higher than at the oral cavity and that a subset of men with secondary syphilis and prolonged anal lesions may be relatively infectious. Earlier detection and treatment of syphilis, when RPR titres are lower than 1:16, could potentially reduce infectiousness from anal and oral sites.