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

BackgroundTreponema 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 findingsComplete 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/SignificanceThe 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.

Whole genome sequence of the Treponema pallidum subsp. endemicum strain Iraq B: A subpopulation of bejel treponemes contains full-length tprF and tprG genes similar to those present in T. p. subsp. pertenue strains

“…endemicum (TEN). The genome was assembled using the previously described PSGS technique [2,[15][16][17]20,21] and Illumina sequencing. The average coverage depth was greater than 3000× and all sequencing ambiguities were resolved with Sanger sequencing of the corresponding PCR products.…”

“…As shown by Mikalová et al [33], the number of arp repetitions is variable in different samples from the same patient. By contrast, the nucleotide mutation rate of TPA and TPE treponemes has been estimated to be 2.8 x 10 −10 and 4.1 x 10 −10 per site per generation or lower [20,34], suggesting treponemal genome stability for a decade (or decades). The TEN Iraq B sequence was also analyzed with respect to the presence of intrastrain heterogeneity and these sites ( Table 3) were compared with the heterogeneous sites identified in TEN Bosnia A genome in study by Čejková et al [26].…”

“…Whole genome alignment of treponemal sequences was constructed with Geneious [19] and SeqMan (DNASTAR, Madison, WI, USA) software using the following genomes: TEN Iraq B (CP032303.1), TEN Bosnia A (CP007548.1; [2]), TPE CDC-2 (CP002375.1; [16]), TPE Gauthier (CP002376.1; [16]), TPE Samoa D (CP002374.1; [16]), TPE Ghana-051 (CP020365.1; [20]), TPE CDC 2575 (CP020366.1; [20]), TPE LMNP-1 (CP021113.1; [13]), TPE Kampung Dalan K363 (CP024088.1; [21]), TPE Sei Geringging K403 (CP024089.1; [21]), TPE Fribourg-Blanc (CP003902.1; [17]), and TPA SS14 (CP004011.1; [22]). Complete genome sequences, except for chromosomal regions showing recombination (tprK sequences, tRNA-Ile and tRNA-Ala intergenic spacers of both rRNA operons, tprD gene) or containing repetitions (arp, and TP0470 genes), were used to construct a phylogenetic tree.…”

“…Genetic heterogeneity was identified according to the protocol described elsewhere [20,21,26,27]. Briefly, individual Illumina reads were mapped to the final version of the TEN Iraq B genome sequence using SeqMan NGen (v4.1.0) software with default parameters.…”

“…The TEN Iraq B genome was assessed for the presence of intrastrain heterogeneity [20,21,26,27], with a frequency cutoff for minor alleles of 8% or more [20,21]. Altogether, 12 such sites were identified in TEN Iraq B, and the list of heterogeneous sites is shown in Table 3.…”