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

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.梅毒是一项重要的公共卫生问题，近年来其发病率呈逐年上升趋势。通过分子数据解析菌株多样性，对于理解该疾病复发现象的流行病学特征至关重要。本研究针对苍白密螺旋体苍白亚种（Treponema pallidum subsp. pallidum，简称TPA）提出一种新型高分辨多位点序列分型（Multilocus Sequence Typing，简称MLST）方案。我们对直接取自临床样本或兔传代菌株的30株苍白密螺旋体苍白亚种完整基因组与草图基因组进行分析，以筛选合适的分型位点，并在瑞士与法国收集的120份临床样本中对该新型分型方案进行验证。分析结果筛选出三个具备高分辨能力的位点：TP0136、TP0548及TP0705。结合针对大环内酯类耐药的23S核糖体RNA基因（23S rRNA gene）基因突变分析，我们将上述位点作为苍白密螺旋体苍白亚种的MLST分型方案。在临床样本中共检出23种等位基因谱，且大环内酯类耐药样本占比高达80%。相较于既往分型方案，本研究提出的新型MLST方案具备更高的分辨能力，可实现苍白密螺旋体苍白亚种与其他密螺旋体细菌的区分、两大主要进化支（Nichols株与SS14株）之间的鉴别，以及各进化支内部菌株的分型。