Background Pathogenic uncultivable treponemes include the agents of syphilis ( T. pallidum ssp. pallidum, TPA), yaws ( T. pallidum ssp. pertenue, TPE) and endemic syphilis ( T. pallidum ssp. endemicum, TEN). Treponema paraluiscuniculi (TPC) causes rabbit syphilis. Pathogenic treponemes are highly clonal bacteria showing minimal genetic variability in the genome sequence of individual strains.

Methods Five TPA strains (Nichols, SS14, Chicago, Mexico A and DAL-1), three TPE strains (CDC-2, Samoa D and Gauthier) and a one TPC strain Cuniculi A were analysed in this study. All possible combinations of gene alignments were tested on type of selection by Z-test using modified Nei-Gojobori method based on Jukes-Cantor model. Complete deletion was used as a gap treatment and transition/transversion ratio was set to 0.85. Results were considered significant at 5% level.

Results A total of 22 genes were found under positive selection in at least one comparison between treponemal strains. Negative and neutral selection was found in at least one combination for 258 and 206 genes, respectively. While positive selection was identified in genes encoding putative virulence factors, proteins involved in cell structure and cell processes, negative selection was predominantly found in genes encoding components of general metabolism, transport and translation. Neutral selection was detected mainly in genes encoding hypothetical proteins and genes encoding proteins involved in general metabolism.

Conclusions Positively selected genes are candidates for important treponemal virulence factors while negatively selected and conserved genes are likely to encode essential genes. Genes under neutral evolution may indicate genome regions that could be lost during adaptation of pathogen to its host.