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The genomes of eight treponemes including  T. p. pallidum  strains (Nichols, SS14, DAL-1 and Mexico A),  T. p. pertenue  strains (Samoa D, CDC-2 and Gauthier), and the Fribourg-Blanc isolate, were amplified in 133 overlapping amplicons, and the restriction patterns of these fragments were compared. The approximate sizes of the genomes investigated based on this whole genome fingerprinting (WGF) analysis ranged from 1139.3–1140.4 kb, with the estimated genome sequence identity of 99.57–99.98% in the homologous genome regions. Restriction target site analysis, detecting the presence of 1773 individual restriction sites found in the reference Nichols genome, revealed a high genome structure similarity of all strains. The unclassified simian Fribourg-Blanc isolate was more closely related to  T. p. pertenue  than to  T. p. pallidum  strains. Most of the genetic differences between  T. p. pallidum  and  T. p. pertenue  strains were accumulated in six genomic regions. These genome differences likely contribute to the observed differences in pathogenicity between  T. p. pallidum  and  T. p. pertenue  strains. These regions of sequence divergence could be used for the molecular detection and discrimination of syphilis and yaws strains.

Genome Analysis of Treponema pallidum subsp. pallidum and subsp. pertenue Strains: Most of the Genetic Differences Are Localized in Six Regions