Whole genome sequences of Treponema pallidum subsp. endemicum isolated from Cuban patients: The non-clonal character of isolates suggests a persistent human infection rather than a single outbreak

Abstract

Bejel (endemic syphilis) is a neglected non-venereal disease caused by Treponema pallidum subsp. endemicum (TEN). Although it is mostly present in hot, dry climates, a few cases have been found outside of these areas. The aim of this work was the sequencing and analysis of TEN isolates obtained from “syphilis patients” in Cuba, which is not considered an endemic area for bejel. Genomes were obtained by pool segment genome sequencing or direct sequencing methods, and the bioinformatics analysis was performed according to an established pipeline. We obtained four genomes with 100%, 81.7%, 52.6%, and 21.1% breadth of coverage, respectively. The sequenced genomes revealed a non-clonal character, with nucleotide variability ranging between 0.2–10.3 nucleotide substitutions per 100 kbp among the TEN isolates. Nucleotide changes affected 27 genes, and the analysis of the completely sequenced genome also showed a recombination event between tprC and tprI, in TP0488 as well as in the intergenic region between TP0127–TP0129. Despite limitations in the quality of samples affecting breadth of sequencing coverage, the determined non-clonal character of the isolates suggests a persistent infection in the Cuban population rather than a single outbreak caused by imported case.

Redefining the treponemal history through pre-Columbian genomes from Brazil

“…As syphilis has been the central focus of Treponema research, the endemic treponematoses have received less attention 2 , 40 . Contrary to yaws and syphilis, both of which have been previously found in Old and New World contexts from the early modern period 3 – 6 , this newly reconstructed genome represents the first TEN-like pathogen isolated from archaeological remains, and the only ancient comparison to the current set of eight published bejel genomes 17 , 38 , 41 , 42 . Recent cases have shown that treponematoses are occasionally transmitted in an atypical manner for their genetically confirmed subspecies, and have challenged their geographical and symptom-driven categorizations 43 – 45 .…”

“…We selected all eight publicly available TEN genomes, all of which have more than 99.4% genome coverage, with the exception of C77 17 (81.4%). We selected 30 TPE genomes (Supplementary Table 3 ).…”

“…Additionally, we used tested sequencing and posterior analysis methodologies 17 , 42 to obtain higher coverage and more reliable modern T. pallidum genomes. Where possible, assembly files were obtained rather than raw data (Supplementary Table 3 ).…”

“…This re-emerging threat has led to many modern genetic and medical studies 8 , 13 – 15 . The closely related T. pallidum subspecies T. pallidum pallidum (TPA), T. pallidum pertenue (TPE) and T. pallidum endemicum (TEN)—responsible for syphilis, yaws and bejel, respectively—have highly similar genome sequences that differ by approximately 0.03% 16 , 17 . Today, bejel is geographically concentrated in arid, hot environments, especially the eastern Mediterranean and western Asia, whereas yaws is mainly found in the humid, warm tropics such as Africa or South America 18 .…”

Inferring patterns of recombination and divergence with ancient and modern treponemal genomes

“…Prior to the final phylogenetic analyses, genes identified by PIM as recombinant were excluded from the multiple genome alignment. To avoid introducing a potential bias into the phylogenetic signal, 3 genes ( tp0897, tp0316, tp0317 ), which contain repetitive regions and have previously been reported as hypervariable and/or under gene conversion (Pinto et al 2016; Liu et al 2019;Addetia et al 2020); (Strouhal et al 2018; Vrbová et al 2022) and thus induce recombination-like effects in mapping, were also removed. As the tp0317 gene is embedded inside the tp0316 gene, and moreover the coordinates from the BosniaA reference genome for tp0316 spanned a longer region compared to the other reference genomes, tp0316 and tp0317 were removed according to the BosniaA reference genome coordinates for tp0316 .…”