Objectives To determine whether the 23S ribosomal RNA (rRNA) A2058G and A2059G mutations that confer macrolide resistance are present among southern African strains of Treponema pallidum and to determine their subtype distribution.

Methods 117 genital ulcer specimens, collected between March 2005 and April 2010 in South Africa and Lesotho and previously determined to be positive for T pallidum DNA by molecular testing, were retested using a commercial real-time PCR assay. Those specimens that were still positive for T pallidum DNA were screened for the macrolide resistance-encoding point mutations in the 23S rRNA gene using rapid PCR-based restriction digest assays. Molecular characterisation of two variable treponemal genes, arp and tpr, was used to subtype the T pallidum strains.

Results 1 of 100 T pallidum-positive specimens, collected in Lesotho, contained the A2058G macrolide resistance-encoding 23S rRNA gene mutation, whereas the A2059G mutation was absent. It was possible to fully type 97/100 of all T pallidum DNA-positive samples. A total of nine arp repeat sizes, nine tpr patterns and a combined total of 20 subtypes were identified. Overall, the most common subtypes were 14d (32%), followed by 17d (12%), 14a (10%), 14b (8%), 22b (6%) and 14i (5%). Subtypes 14d and 14a were the predominant subtypes in samples from South Africa (43%) and Lesotho (22%), respectively.

Conclusions Macrolide resistance among T pallidum strains appears to be uncommon in southern Africa. Although a high degree of genetic heterogeneity was observed among the strains tested, T pallidum subtype 14d appears to be the predominant circulating strain.