BACKGROUND: Treponema pallidum subsp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). An unusual human TEN 11q/j isolate was obtained from a syphilis-like primary genital lesion from a patient that returned to France from Pakistan. METHODOLOGY/PRINCIPAL FINDINGS: The TEN 11q/j isolate was characterized using nested PCR followed by Sanger sequencing and/or direct Illumina sequencing. Altogether, 44 chromosomal regions were analyzed. Overall, the 11q/j isolate clustered with TEN strains Bosnia A and Iraq B as expected from previous TEN classification of the 11q/j isolate. However, the 11q/j sequence in a 505 bp-long region at the TP0488 locus was similar to Treponema pallidum subsp. pallidum (TPA) strains, but not to TEN Bosnia A and Iraq B sequences, suggesting a recombination event at this locus. Similarly, the 11q/j sequence in a 613 bp-long region at the TP0548 locus was similar to Treponema pallidum subsp. pertenue (TPE) strains, but not to TEN sequences. CONCLUSIONS/SIGNIFICANCE: A detailed analysis of two recombinant loci found in the 11q/j clinical isolate revealed that the recombination event occurred just once, in the TP0488, with the donor sequence originating from a TPA strain. Since TEN Bosnia A and Iraq B were found to contain TPA-like sequences at the TP0548 locus, the recombination at TP0548 took place in a treponeme that was an ancestor to both TEN Bosnia A and Iraq B. The sequence of 11q/j isolate in TP0548 represents an ancestral TEN sequence that is similar to yaws-causing treponemes. In addition to the importance of the 11q/j isolate for reconstruction of the TEN phylogeny, this case emphasizes the possible role of TEN strains in development of syphilis-like lesions.

CEITEC Central European Institute of Technology Masaryk University Brno Czech Republic National Centre for Biomolecular Research Masaryk University Brno Czech Republic

Centre des MST Hôpital Saint Louis AP HP Paris France

Department of Biology Faculty of Medicine Masaryk University Brno Czech Republic

Institut Cochin U1016 Laboratoire de Dermatologie CNR Syphilis Faculté de Médecine Université Sorbonne Paris Descartes Paris France

Institut Cochin U1016 Laboratoire de Dermatologie CNR Syphilis Faculté de Médecine Université Sorbonne Paris Descartes Paris France Service de Bactériologie Groupe Hospitalier Paris Centre Cochin Hôtel Dieu Broca Paris France

Institut Cochin U1016 Laboratoire de Dermatologie CNR Syphilis Faculté de Médecine Université Sorbonne Paris Descartes Paris France Service de Dermatologie Vénéréologie Hôpital Cochin Pavillon Tarnier AP HP Paris France

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