Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina

BackgroundSyphilis 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. MethodsPeople 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. FindingsTp 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. InterpretationTp circulating in South America is closely related to dominant global sublineages. Increased tprK diversity in the SS14 lineage may influence Tps 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. FundingGates Foundation INV-036560 (to A.S.) and NIH/NIAID R01AI139265 (to J.D.K). Research in contextO_ST_ABSEvidence before this studyC_ST_ABSAlthough whole genome sequencing (WGS) and genomic epidemiology have contributed to an understanding of the global diversity of Treponema pallidum (Tp), very few strains from South America have been sequenced to date. On January 6th, 2026, we performed a PubMed search including terms "syphilis genomic epidemiology", "South America", "Treponema pallidum", and "Argentina". We excluded studies of ancient Tp samples found in South American archeological sites. A single Tp sample from Argentina was originally sequenced in 2016 and included in subsequent analyses of global diversity. Nine Peruvian samples were previously sequenced in a study of global diversity on six continents. Thirty-three samples from Cali, Colombia were predominantly SS14-lineage and genotypic macrolide resistance was found in half of strains. Additionally, studies of Tp in Buenos Aires using a multi-locus sequence typing approach have shown circulation of strains belonging to both Nichols and SS14 lineages, with an increasing rate of macrolide resistance over time. Aside from a report of inter-strain recombination of Tp in an individual infected with both Nichols- and SS14-lineage strains, no studies have found intra-host evolution of Tp outside of the T. pallidum repeat (tpr) family or acidic repeat proteins. Five previous studies have examined tprK in clinical specimens and consistently shown increased tprK diversity in specimens associated with secondary syphilis compared to primary syphilis lesions. One prior study has shown that loss of tprK donor cassettes is associated with reduced tprK diversity, consistent with results from in vitro experiments. A single study has shown that tprK sequence content is more similar in samples with a suspected epidemiologic link, though no prior studies have looked at tprK diversity in the context of known syphilis transmission events. Added value of this studyThis study is the first to use WGS to comprehensively examine Tp transmission in a large South American city, yielding 96 samples from 70 individuals. We also add the first contemporary Tp genomes from Brazil. In contrast to findings from England, Australia, and other high-income countries, no Tp sublineages are associated with particular demographic groups or sexual networks in Buenos Aires. Two of seventy patients were co-infected with both Nichols- and SS14-lineage strains, showing the previously unappreciated frequency of conditions that permit inter-strain recombination-driven diversification of Tp. This study also reveals novel aspects of Tp pathogenesis, including recovery of specific intra-host tp0006 point mutations from different specimen types and lineage-specific differences in tprK diversity. We also develop methods for the analysis of tprK relatedness between samples and demonstrate that tprK sequences are more similar in samples from individuals within intra-household syphilis transmission chains compared to those from epidemiologically unrelated individuals. Implications of all the available evidenceTp strains circulating in Buenos Aires,are genetically similar to those circulating worldwide and in Brazil and Peru but are noteworthy for the low (but rising) rate of macrolide resistance. Lineage-specific patterns of tprK antigenic variation could result in differences between Nichols- and SS14-lineage strains interactions with the host immune system. Finally, we show that tprK profiling holds promise to identify samples from within a syphilis transmission chain and could play an important role in public health.