Background Treponema pallidum ssp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). The TEN Bosnia A strain was isolated in 1950 from a patient’s penile lesion in northeastern Bosnia.

Methods To define genetic differences between TEN Bosnia A and other pathogenic treponemes including the agents of syphilis ( T. pallidum ssp. pallidum, TPA)and yaws ( T. pallidum ssp. pertenue, TPE), a high quality sequence of the Bosnia A genome was determined using 454-pyrosequencing, Illumina, SOLiD and traditional Sanger sequencing. Combined average coverage of these sequencing methods was greater than 340x.

Results Compared to other TPA and TPE treponemes, the genome of Bosnia A (1,137,653 bp) was smaller in size (∼2 kb) but structurally almost identical to other TPA and TPE strains. The Bosnia A genome clustered with TPE strains (nucleotide identity excluding indels ranged between 99.91 – 99.94%) while TPAstrains were more distantly related (99.79 – 99.82%). More than 400 Bosnia A-specific nt changes (i.e. sequences different from TPA and TEN genomes) were found as the result of our analysis.

Conclusions The Bosnia A genome showed similar genetic characteristics as other TPA and TPE strains. Genetic differences found between TPA strains and Bosnia A genome could be used for identification of potential virulence factors of syphis treponemes. Moreover, genetic changes specific for Bosnia A genome could help develop molecular diagnostic tests for endemic syphilis.