Lieberman, N. A. P.; Garcia, L. N.; Mohamed Bakhash, S. A.; Furlong, J.; Nunley, B. E.; Rabinovich, A.; Pardal, P. F.; Leiro, V.; Xie, H.; Aghakhanian, F.; Passos, M. R. L.; Campos Arze, W. N.; Boechat Andrade, H.; Vargas, S.; Konda, K. A.; Reyes-Diaz, M.; Caceres, C.; Klausner, J. D.; Parr, J. B.; Sena, A. C.; Manathunge, A.; Giacani, L.; Altcheh, J.; Greninger, A. L.

Background: Syphilis rates are rising globally, with increases in congenital syphilis in South America particularly concerning. The characterization of contemporary South American Treponema pallidum (Tp) strains is crucial to syphilis vaccine development, yet few genomic epidemiology studies have focused on this region. Here, we performed whole genome sequencing of Tp from Buenos Aires, Argentina, as well as deep sequencing of the hypervariable tprK locus, which is critical to Tp immune evasion. Methods: People with primary, secondary, or congenital syphilis were enrolled at two clinics in Buenos Aires between October 2018 and January 2023, including individuals associated with intra-household transmission. Tp DNA from swabs was quantified by tp0574 qPCR, and whole-genome sequencing was performed on samples with sufficient treponemal burden. Tp reads were assembled to the SS14 strain reference genome, recombinant regions masked, and a core genome phylogeny was generated. Full-length tprK was sequenced using PacBio reads. Findings: Tp genomes were recovered from 96 samples from 70 individuals in Buenos Aires and primarily belonged to globally dominant SS14 sublineage-1 and Nichols sublineage-8, as did Tp recovered from contemporary samples from Brazil (n=8). Peruvian samples (n=3) all belonged to sublineage-1. Two individuals from Buenos Aires had co-infections with Nichols- and SS14-lineage strains. Macrolide resistance via A2058G mutation occurred in 27/70 (39%) samples. Across 56 samples, tprK allelic diversity was significantly increased in secondary syphilis, oral lesions, and SS14-lineage strains compared to primary syphilis, anogenital lesions, and Nichols-lineage strains, respectively. Increased tprK diversity in SS14-lineage strains is driven by an enhanced repertoire of V7-specific donor sequences. Using multiple approaches, tprK sequences from intra-household transmission events were more similar than unrelated samples with identical core genomes. Interpretation: Tp circulating in South America is closely related to dominant global sublineages. Increased tprK diversity in the SS14 lineage may influence Tp's ability to escape host adaptive immunity. We confirmed that tprK profiling is a promising tool to elucidate syphilis transmission networks. This study underscores the utility of genomics to yield insights into Tp pathogenesis.