Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Ghana, Africa: Identical genome sequences in samples isolated more than 7 years apart

Abstract

Background: Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multi-stage disease, endemic in tropical regions of Africa, Asia, Oceania, and South America. To date, four TPE strains have been completely sequenced including three TPE strains of human origin (Samoa D, CDC-2, and Gauthier) and one TPE strain (Fribourg-Blanc) isolated from a baboon. All TPE strains are highly similar to T. pallidum subsp. pallidum (TPA) strains. The mutation rate in syphilis and related treponemes has not been experimentally determined yet.

Methodology/principal findings: Complete genomes of two TPE strains, CDC 2575 and Ghana-051, that infected patients in Ghana and were isolated in 1980 and 1988, respectively, were sequenced and analyzed. Both strains had identical consensus genome nucleotide sequences raising the question whether TPE CDC 2575 and Ghana-051 represent two different strains. Several lines of evidence support the fact that both strains represent independent samples including regions showing intrastrain heterogeneity (13 and 5 intrastrain heterogeneous sites in TPE Ghana-051 and TPE CDC 2575, respectively). Four of these heterogeneous sites were found in both genomes but the frequency of alternative alleles differed. The identical consensus genome sequences were used to estimate the upper limit of the yaws treponeme evolution rate, which was 4.1 x 10-10 nucleotide changes per site per generation.

Conclusions/significance: The estimated upper limit for the mutation rate of TPE was slightly lower than the mutation rate of E. coli, which was determined during a long-term experiment. Given the known diversity between TPA and TPE genomes and the assumption that both TPA and TPE have a similar mutation rate, the most recent common ancestor of syphilis and yaws treponemes appears to be more than ten thousand years old and likely even older.

Fig 1. An origin of the analyzed samples including the time and place of isolation, clinical data and the number of passages in experimental animals.

Both patients with TPE infection were infected in Ghana and the time between sample collections was 7 years and 3 months.

Fig 2. An unrooted tree constructed from whole genome sequence alignments from available TPE and TEN genomes.

The tree was constructed using the Maximum Likelihood method based on Tamura-Nei model and MEGA7 software [15]. Bootstrap values based on 1,000 replications are shown next to the branches. A. An unrooted tree constructed from the whole genome sequence alignment of TPE and TEN genome sequences. The bar scale corresponds to a difference of 0.00010 nucleotides. B. An unrooted tree constructed from the whole genome sequence alignment of TPE and TEN genome sequences. The bar scale corresponds to a difference of 0.00005 nucleotides. tprK sequences, both rRNA operons, tprD, arp, and TP0470 genes were omitted from the analysis. Deletion of these regions resulted in a modified tree topology due to: (1) differences between the two possible constitutional states for the rRNA operons [19], (2) the presence of two tprD alleles in the TPE population (tprD and tprD2; [20]), and (3) differences in the number of repetitions in the arp and TP0470 genes.