Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina
Abstract 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...
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2026
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| author | Nicole A.P. Lieberman Luciana García Shah A.K. Mohamed Bakhash Jeffrey C. Furlong B. Ethan Nunley Andrés Rabinovich Patricia Fernández Pardal Viviana Leiro Hong Xie Farhang Aghakhanian Mauro Romero Leal Passos Wilma Nancy Campos Arze Hugo Boechat Andrade Silver K. Vargas Kelika A. Konda Michael Reyes-Diaz Carlos F. Cáceres Jeffrey D. Klausner Jonathan B Parr Arlene C. Sena Ariyaratne Manathunge Lorenzo Giacani Jaime Altcheh Alexander L. Greninger |
| author_browse | Alexander L. Greninger Andrés Rabinovich Ariyaratne Manathunge Arlene C. Sena B. Ethan Nunley Carlos F. Cáceres Farhang Aghakhanian Hong Xie Hugo Boechat Andrade Jaime Altcheh Jeffrey C. Furlong Jeffrey D. Klausner Jonathan B Parr Kelika A. Konda Lorenzo Giacani Luciana García Mauro Romero Leal Passos Michael Reyes-Diaz Nicole A.P. Lieberman Patricia Fernández Pardal Shah A.K. Mohamed Bakhash Silver K. Vargas Viviana Leiro Wilma Nancy Campos Arze |
| author_facet | Nicole A.P. Lieberman Luciana García Shah A.K. Mohamed Bakhash Jeffrey C. Furlong B. Ethan Nunley Andrés Rabinovich Patricia Fernández Pardal Viviana Leiro Hong Xie Farhang Aghakhanian Mauro Romero Leal Passos Wilma Nancy Campos Arze Hugo Boechat Andrade Silver K. Vargas Kelika A. Konda Michael Reyes-Diaz Carlos F. Cáceres Jeffrey D. Klausner Jonathan B Parr Arlene C. Sena Ariyaratne Manathunge Lorenzo Giacani Jaime Altcheh Alexander L. Greninger |
| author_sort | Nicole A.P. Lieberman |
| collection | Producción científica |
| description | Abstract 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 (WGS) 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. Hybrid capture WGS was performed and a core genome phylogeny generated. K-mer-based methods using full-length tprK PacBio long reads were used to uncover differences in diversity and detect Tp transmission. Findings Tp genomes were recovered from 70 individuals in Buenos Aires and primarily belonged to globally dominant SS14 sublineage-1 and Nichols sublineage-8, as did Tp 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, 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 diversity in SS14-lineage strains is driven by an enhanced repertoire of V7-specific donor sequences. tprK sequences from intra-household transmissions 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 immunity. tprK profiling is a promising tool to elucidate syphilis transmission networks. This study underscores the utility of genomics to yield insights into Tp pathogenesis. Research in context Evidence before this study Although 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 6 th , 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. 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 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 study This 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 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 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 evidence Tp 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. |
| format | Article |
| id | oai:cris.upeu.edu.pe:20.500.15037/1158 |
| institution | UPeU |
| language | English |
| publishDate | 2026 |
| publishDateRange | 2026 |
| publishDateSort | 2026 |
| record_format | dspace |
| spelling | oai:cris.upeu.edu.pe:20.500.15037/11582026-10-30T16:15:17ZLineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, ArgentinaNicole A.P. LiebermanLuciana GarcíaShah A.K. Mohamed BakhashJeffrey C. FurlongB. Ethan NunleyAndrés RabinovichPatricia Fernández PardalViviana LeiroHong XieFarhang AghakhanianMauro Romero Leal PassosWilma Nancy Campos ArzeHugo Boechat AndradeSilver K. VargasKelika A. KondaMichael Reyes-DiazCarlos F. CáceresJeffrey D. KlausnerJonathan B ParrArlene C. SenaAriyaratne ManathungeLorenzo GiacaniJaime AltchehAlexander L. GreningerDiversification (marketing strategy)Economic geographyGeographyProfiling (computer programming)Transmission (telecommunications)Diversity (politics)Evolutionary biologyGenetic diversityBiologyEconomicsYield (engineering)Lineage (genetic)EcologyGenomicsEconomyPopulationDevelopment economicsGlobalizationDiversification (marketing strategy)Profiling (computer programming)Transmission (telecommunications)Diversity (politics)Genetic diversityYield (engineering)Health Sciences Medicine Physiology Syphilis Diagnosis and TreatmentLife Sciences Immunology and Microbiology Microbiology Reproductive tract infections researchHealth Sciences Medicine Epidemiology Virology and Viral DiseasesAbstract 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 (WGS) 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. Hybrid capture WGS was performed and a core genome phylogeny generated. K-mer-based methods using full-length tprK PacBio long reads were used to uncover differences in diversity and detect Tp transmission. Findings Tp genomes were recovered from 70 individuals in Buenos Aires and primarily belonged to globally dominant SS14 sublineage-1 and Nichols sublineage-8, as did Tp 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, 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 diversity in SS14-lineage strains is driven by an enhanced repertoire of V7-specific donor sequences. tprK sequences from intra-household transmissions 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 immunity. tprK profiling is a promising tool to elucidate syphilis transmission networks. This study underscores the utility of genomics to yield insights into Tp pathogenesis. Research in context Evidence before this study Although 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 6 th , 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. 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 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 study This 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 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 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 evidence Tp 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.Articlehttps://pubmed.ncbi.nlm.nih.gov/41659500https://www.biorxiv.org/content/biorxiv/early/2026/01/30/2026.01.29.702707.full.pdfhttps://doi.org/10.64898/2026.01.29.70270710.64898/2026.01.29.702707https://hdl.handle.net/20.500.15037/1158W7126414147en2026-01-302026-06-13T09:48:00Z2026-06-13T09:48:00Z |
| spellingShingle | Diversification (marketing strategy) Economic geography Geography Profiling (computer programming) Transmission (telecommunications) Diversity (politics) Evolutionary biology Genetic diversity Biology Economics Yield (engineering) Lineage (genetic) Ecology Genomics Economy Population Development economics Globalization Diversification (marketing strategy) Profiling (computer programming) Transmission (telecommunications) Diversity (politics) Genetic diversity Yield (engineering) Health Sciences Medicine Physiology Syphilis Diagnosis and Treatment Life Sciences Immunology and Microbiology Microbiology Reproductive tract infections research Health Sciences Medicine Epidemiology Virology and Viral Diseases Nicole A.P. Lieberman Luciana García Shah A.K. Mohamed Bakhash Jeffrey C. Furlong B. Ethan Nunley Andrés Rabinovich Patricia Fernández Pardal Viviana Leiro Hong Xie Farhang Aghakhanian Mauro Romero Leal Passos Wilma Nancy Campos Arze Hugo Boechat Andrade Silver K. Vargas Kelika A. Konda Michael Reyes-Diaz Carlos F. Cáceres Jeffrey D. Klausner Jonathan B Parr Arlene C. Sena Ariyaratne Manathunge Lorenzo Giacani Jaime Altcheh Alexander L. Greninger Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina |
| title | Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina |
| title_full | Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina |
| title_fullStr | Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina |
| title_full_unstemmed | Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina |
| title_short | Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina |
| title_sort | lineage specific tprk diversification and treponema pallidum transmission dynamics in buenos aires argentina |
| topic | Diversification (marketing strategy) Economic geography Geography Profiling (computer programming) Transmission (telecommunications) Diversity (politics) Evolutionary biology Genetic diversity Biology Economics Yield (engineering) Lineage (genetic) Ecology Genomics Economy Population Development economics Globalization Diversification (marketing strategy) Profiling (computer programming) Transmission (telecommunications) Diversity (politics) Genetic diversity Yield (engineering) Health Sciences Medicine Physiology Syphilis Diagnosis and Treatment Life Sciences Immunology and Microbiology Microbiology Reproductive tract infections research Health Sciences Medicine Epidemiology Virology and Viral Diseases |
| topic_facet | Diversification (marketing strategy) Economic geography Geography Profiling (computer programming) Transmission (telecommunications) Diversity (politics) Evolutionary biology Genetic diversity Biology Economics Yield (engineering) Lineage (genetic) Ecology Genomics Economy Population Development economics Globalization Diversification (marketing strategy) Profiling (computer programming) Transmission (telecommunications) Diversity (politics) Genetic diversity Yield (engineering) Health Sciences Medicine Physiology Syphilis Diagnosis and Treatment Life Sciences Immunology and Microbiology Microbiology Reproductive tract infections research Health Sciences Medicine Epidemiology Virology and Viral Diseases |
| url | https://pubmed.ncbi.nlm.nih.gov/41659500 https://www.biorxiv.org/content/biorxiv/early/2026/01/30/2026.01.29.702707.full.pdf https://doi.org/10.64898/2026.01.29.702707 https://hdl.handle.net/20.500.15037/1158 |
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