Analysis of Treponema pallidum Strains From China Using Improved Methods for Whole-Genome Sequencing From Primary Syphilis Chancres

Abstract Background Whole-genome sequencing (WGS) of Treponema pallidum subspecies pallidum (TPA) has been constrained by the lack of in vitro cultivation methods for isolating spirochetes from patient samples. Methods We built upon recently developed enrichment methods to sequence TPA directly from primary syphilis chancre swabs collected in Guangzhou, China. Results By combining parallel, pooled whole-genome amplification with hybrid selection, we generated high-quality genomes from 4 of 8 chancre-swab samples and 2 of 2 rabbit-passaged isolates, all subjected to challenging storage conditions. Conclusions This approach enabled the first WGS of Chinese samples without rabbit passage and provided insights into TPA genetic diversity in China. Parallel, pooled whole-genome amplification and hybrid selection enabled whole-genome sequencing of Treponema pallidum DNA extracted directly from primary syphilis chancre swabs, despite challenging storage conditions. Phylogenomic analysis revealed diverse strains, including the first Nichols-like genome reported from China to date.