Background Next-generation sequencing techniques, besides determination of complete genome sequences and interstrain variability, can assess variability within individual bacterial strains. Here we examined intrastrain heterogeneity in two strains of T. pallidum ssp. pallidum, the agent of syphilis.

Methods To ascertain intrastrain heterogeneity within Nichols and SS14 strains, whole-genome sequencing Illumina reads were used. Individual reads were mapped to complete genomes using Borrows-Wheeler Aligner. To determine the allele frequency of mapped reads for every genome position, the SAMtools package and Perl script were applied and heterogenous positions showing at least six independent reads calling for an alternative allele were further examined. To distinguish true variants from sequencing errors, each heterogenous position was visually evaluated.

Results Altogether, 17 and 31 intrastrain variable positions were found in the unique regions of Nichols and SS14 genomes, respectively. Only 2 positions in each strain were located in intergenic regions. The variable positions of the Nichols and SS14 strains altered 16 and 29 genes, respectively, while four genes (coding for cell division protein, TprB protein, polymerase A and putative lipoprotein) were altered in both genomes at the same positions. Generally, genes for hypothetical proteins and putative membrane proteins, and transporters showed intrastrain heterogeneity in both genomes. Moreover, for the SS14 strain, variable positions in genes coding for DNA repair mechanism and motility were found.

Conclusion The identified variable regions of treponemal genomes appear to provide a selective advantage in host-pathogen interaction. To determine the extent of intrastrain heterogeneity in other pathogenic treponemes, additional completed genomes will be evaluated.