{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T22:38:33Z","timestamp":1777588713304,"version":"3.51.4"},"posted":{"date-parts":[[2026,1,30]]},"group-title":"Microbiology","reference-count":48,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T00:00:00Z","timestamp":1769731200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Gates Foundation","award":["INV-036560"],"award-info":[{"award-number":["INV-036560"]}]},{"name":"NIH\/NIAID","award":["R01AI139265"],"award-info":[{"award-number":["R01AI139265"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,4,3]]},"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n \n Syphilis rates are rising globally, with increases in congenital syphilis in South America particularly concerning. The characterization of contemporary South American\n Treponema pallidum (Tp)<\/jats:italic>\n strains is crucial to syphilis vaccine development, yet few genomic epidemiology studies have focused on this region. Here, we performed whole genome sequencing (WGS) of\n Tp<\/jats:italic>\n from Buenos Aires, Argentina, as well as deep sequencing of the hypervariable\n tprK<\/jats:italic>\n locus, which is critical to\n Tp<\/jats:italic>\n immune evasion.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n 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. Hybrid capture WGS was performed and a core genome phylogeny generated. K-mer-based methods using full-length\n tprK<\/jats:italic>\n PacBio long reads were used to uncover differences in diversity and detect\n Tp<\/jats:italic>\n transmission.\n <\/jats:p>\n <\/jats:sec>\n \n Findings<\/jats:title>\n \n Tp<\/jats:italic>\n genomes were recovered from 70 individuals in Buenos Aires and primarily belonged to globally dominant SS14 sublineage-1 and Nichols sublineage-8, as did\n Tp<\/jats:italic>\n from Brazil (n=8). Peruvian samples (n=3) all belonged to sublineage-1. Two individuals from Argentina had co-infections with Nichols- and SS14-lineage strains. Macrolide resistance via A2058G occurred in 27\/70 (38.6%) samples. Across 56 samples,\n tprK<\/jats:italic>\n 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 diversity in SS14-lineage strains is driven by an enhanced repertoire of V7-specific donor sequences.\n tprK<\/jats:italic>\n sequences from intra-household transmissions were more similar than unrelated samples with identical core genomes.\n <\/jats:p>\n <\/jats:sec>\n \n Interpretation<\/jats:title>\n \n Tp<\/jats:italic>\n circulating in South America is closely related to dominant global sublineages. Increased\n tprK<\/jats:italic>\n diversity in the SS14 lineage may influence\n Tp\u2019s<\/jats:italic>\n ability to escape host immunity.\n tprK<\/jats:italic>\n profiling is a promising tool to elucidate syphilis transmission networks. This study underscores the utility of genomics to yield insights into\n Tp<\/jats:italic>\n pathogenesis.\n <\/jats:p>\n <\/jats:sec>\n \n Research in context<\/jats:title>\n \n Evidence before this study<\/jats:title>\n \n Although whole genome sequencing (WGS) and genomic epidemiology have contributed to an understanding of the global diversity of\n Treponema pallidum<\/jats:italic>\n (\n Tp<\/jats:italic>\n ), very few strains from South America have been sequenced to date. On January 6\n th<\/jats:sup>\n , 2026, we performed a PubMed search including terms \u201csyphilis genomic epidemiology\u201d, \u201cSouth America\u201d, \u201c\n Treponema pallidum<\/jats:italic>\n \u201d, and \u201cArgentina\u201d. We excluded studies of ancient\n Tp<\/jats:italic>\n samples found in South American archeological sites. A single\n Tp<\/jats:italic>\n 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\n Tp<\/jats:italic>\n 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. Five previous studies have examined\n tprK<\/jats:italic>\n in clinical specimens and consistently shown increased\n tprK<\/jats:italic>\n diversity in specimens associated with secondary syphilis compared to primary syphilis lesions. One study has shown that loss of\n tprK<\/jats:italic>\n donor cassettes is associated with reduced\n tprK<\/jats:italic>\n diversity, consistent with results from\n in vitro<\/jats:italic>\n experiments. A single study has shown that\n tprK<\/jats:italic>\n sequence content is more similar in samples with a suspected epidemiologic link, though no prior studies have looked at\n tprK<\/jats:italic>\n diversity in the context of known syphilis transmission events.\n <\/jats:p>\n <\/jats:sec>\n \n Added value of this study<\/jats:title>\n \n This study is the first to use WGS to comprehensively examine\n Tp<\/jats:italic>\n transmission in a large South American city, yielding 96 samples from 70 individuals. We also add the first contemporary\n Tp<\/jats:italic>\n genomes from Brazil. In contrast to findings from England, Australia, and other high-income countries, no\n Tp<\/jats:italic>\n sublineages are associated with 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\n Tp<\/jats:italic>\n . This study also reveals novel aspects of\n Tp<\/jats:italic>\n pathogenesis, including lineage-specific differences in\n tprK<\/jats:italic>\n diversity. We also develop methods for the analysis of\n tprK<\/jats:italic>\n relatedness between samples and demonstrate that\n tprK<\/jats:italic>\n sequences are more similar in samples from individuals within intra-household syphilis transmission chains compared to those from epidemiologically unrelated individuals.\n <\/jats:p>\n <\/jats:sec>\n \n Implications of all the available evidence<\/jats:title>\n \n Tp<\/jats:italic>\n 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\n tprK<\/jats:italic>\n antigenic variation could result in differences between Nichols- and SS14-lineage strains\u2019 interactions with the host immune system. Finally, we show that\n tprK<\/jats:italic>\n profiling holds promise to identify samples from within a syphilis transmission chain and could play an important role in public health.\n <\/jats:p>\n <\/jats:sec>\n <\/jats:sec>","DOI":"10.64898\/2026.01.29.702707","type":"posted-content","created":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T03:05:19Z","timestamp":1769828719000},"source":"Crossref","is-referenced-by-count":1,"title":["Lineage-specific\n tprK<\/i>\n diversification and\n Treponema pallidum<\/i>\n transmission dynamics in Buenos Aires, Argentina"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9334-8150","authenticated-orcid":false,"given":"Nicole A.P.","family":"Lieberman","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luciana N.","family":"Garcia","sequence":"additional","affiliation":[{"name":"Servicio Parasitolog\u00eda- Chagas, Hospital de Ni\u00f1os Ricardo Gutierrez, Capital Federal, Buenos Aires, Argentina"},{"name":"Instituto Multidisciplinario de Investigaciones en Patolog\u00edas Pedi\u00e1tricas (IMIPP), CONICET, Buenos Aires, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shah A. 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Arze","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Niter\u00f3i, RJ, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugo Boechat","family":"Andrade","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Niter\u00f3i, RJ, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silver K.","family":"Vargas","sequence":"additional","affiliation":[{"name":"Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelika A.","family":"Konda","sequence":"additional","affiliation":[{"name":"Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru"},{"name":"Division of Infectious 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