The hare syphilis agent is related to, but distinct from, the treponeme causing rabbit syphilis

Abstract

The treponemes infecting lagomorphs include Treponema paraluisleporidarum ecovar Cuniculus (TPeC) and ecovar Lepus (TPeL), infecting rabbits and hares, respectively. In this study, we described the first complete genome sequence of TPeL, isolate V3603-13, from an infected mountain hare (Lepus timidus) in Sweden. In addition, we determined 99.0% of the genome sequence of isolate V246-08 (also from an infected mountain hare, Sweden) and 31.7% of the genome sequence of isolate Z27 A77/78 (from a European hare, Lepus europeaus, The Netherlands). The TPeL V3603-13 genome had considerable gene synteny with the TPeC Cuniculi A genome and with the human pathogen T. pallidum, which causes syphilis (ssp. pallidum, TPA), yaws (ssp. pertenue, TPE) and endemic syphilis (ssp. endemicum, TEN). Compared to the TPeC Cuniculi A genome, TPeL V3603-13 contained four insertions and 11 deletions longer than three nucleotides (ranging between 6 and2,932 nts). In addition, there were 25 additional indels, from one to three nucleotides long, altogether spanning 36 nts. The number of single nucleotide variants (SNVs) between TPeC Cuniculi A and TPeL V3603-13 were represented by 309 nucleotide differences. Major proteome coding differences between TPeL and TPeC were found in the tpr gene family, and (predicted) genes coding for outer membrane proteins, suggesting that these components are essential for host adaptation in lagomorph syphilis. The phylogeny revealed that the TPeL sample from the European brown hare was more distantly related to TPeC Cuniculi A than V3603-13 and V246-08.

Fig 1. An overview of genome differences between TPeL V3603-13 and TPeC Cuniculi A.

Insertions and deletions are shown above and below the schematic representation of the TPeL isolate V3603-13 chromosome, respectively. Green areas represent sequentially diverse regions, and the lengths of these regions are shown in green letters, while indel lengths are shown in black letters.

Fig 2. Composition of repeat motif regions observed in the TPeL V3603-13 and TPeC Cuniculi A genomes.

Note that repeat motifs determined by Harper et al. [31], and by Šmajs et al. [6], differ, likely due to repeat reshuffling during individual laboratory handling of the Cuniculi A strain.

Fig 3. Molecular phylogeny of TPeL and TPeC samples.

A. The tree was built on partial TP0548 sequences (TPeC Cz-2020 and TPA SS14) [32, 33]. There was a total of 777 positions in the final dataset. B. The tree was built on available genome sequences. There were 355,133 positions in the final dataset. The trees were constructed using the Maximum Likelihood method based on the Tamura-Nei model. Bootstrap support is shown next to the branches. The scale shows the number of substitutions per site. As an outgroup, the TPA SS14 sequence was used. All positions containing gaps and missing data were omitted.

Fig 4. A schematic representation of a possible evolutionary model of the TP0136 locus in TPeL and TPeC treponemes.

The evolution of this region required several steps, including two gene conversion events and one deletion. The part of TP0136 showing a modular structure was not affected during these changes.