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

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% of broad 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 broad 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. Author summary The incidence of venereal syphilis has greatly increased in the last years, however endemic syphilis (bejel) which have been considered as a disease restricted to dry arid areas such as the Sahel and the Middle East, remain as a neglected disease. In Cuba, which is a tropical country, several bejel cases were unexpectedly detected few years ago in “syphilis” patients with no records of travel abroad or sex with foreign partners. In this study, we explored the whole genome sequences from four of the Cuban Treponema pallidum subsp. endemicum (TEN) isolates and the substantial genetic diversity detected among them suggests a persistent infection of TEN within the human population rather than a single outbreak of a TEN isolate introduced from an area where it is typically endemic. This finding has significant implications on this neglected and also possibly tropical disease in terms of geographical/temporal distribution, and highlights the importance of keeping in mind neglected diseases in apparently non-endemic areas.