Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme

Abstract

Syphilis is an important public health problem and an increasing incidence has been noted in recent years. Characterization of strain diversity through molecular data plays a critical role in the epidemiological understanding of this re-emergence. We here propose a new high-resolution multilocus sequence typing (MLST) scheme for Treponema pallidum subsp. pallidum (TPA). We analyzed 30 complete and draft TPA genomes obtained directly from clinical samples or from rabbit propagated strains to identify suitable typing loci and tested the new scheme on 120 clinical samples collected in Switzerland and France. Our analyses yielded three loci with high discriminatory power: TP0136, TP0548, and TP0705. Together with analysis of the 23S rRNA gene mutations for macrolide resistance, we propose these loci as MLST for TPA. Among clinical samples, 23 allelic profiles as well as a high percentage (80% samples) of macrolide resistance were revealed. The new MLST has higher discriminatory power compared to previous typing schemes, enabling distinction of TPA from other treponemal bacteria, distinction between the two main TPA clades (Nichols and SS14), and differentiation of strains within these clades.

No bejel among Surinamese, Antillean and Dutch syphilis diagnosed patients in Amsterdam between 2006–2018 evidenced by multi-locus sequence typing of Treponema pallidum isolates

“…The most prevalent allelic profile found in this study was the SS14-like strain, 1.3.1 (42%), followed by 1.1.1 (19%) in concordance with similar TPA MLST studies [8,12,15,16]. Until now, these two types have been found in every TPA MLST study [13], while all geographic locations (Czech Republic [16], Switzerland [8], France [12], Cuba [15], and the Netherlands) from which the samples were derived also have less common and unique allelic profiles suggesting the combination of global mixing populations and more local mixing of the hosts (S3 Table). To investigate possible bias in the typable versus not (fully) typable samples these groups were compared based on ethnicity, RPR titer, HIV status and syphilis stage.…”

“…Molecular characterization of the samples was performed using the recently developed MLST method by Grillová et al 2018 [8]. This MLST method is based on the partial amplification and sequence analysis of three chromosomal loci; tp0136, tp0548 and tp0705.…”

“…Also both 23S rRNA genes were partly sequenced to check for the A2058G and A2059G mutations associated with macrolide resistance. The partial amplification and sequence analysis using Sanger sequencing was performed as described [8,12]. Sequence analyses were performed using Bionumerics version 7.6.3 (Applied Maths, BioMérieux).…”

“…In 2016, a TEN isolate was identified in France [7]. A recently developed multilocus sequence typing (MLST) scheme [8] enables differentiation between treponemal subspecies as well as the distinction between the two major genetic clades within TPA, Nichols and SS14, and provides strain types within these clades. In 2018, this MLST method was used in Cuba [6] and Japan [9] to retrospectively investigate treponemal subspecies in samples of patients that were diagnosed with syphilis.…”

Ancient bacterial genomes reveal a formerly unknown diversity ofTreponema pallidumstrains in early modern Europe

“…Misdiagnoses occurred until recently, due to the challenges in recognizing T. pallidum infections from other diseases and its subspecies from each other 26 . In the presentday, the treponematoses are largely segregated in medical diagnostics either with traditional serological tests or with the more recently developed multi-locus sequence typing (MLST) schemes [27][28][29][30] . Before the modern genetic classifications were introduced, supporters of the 'unitarian hypothesis' claimed that all treponematoses were in fact one and the same disease 31,32 .…”