{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T00:33:10Z","timestamp":1793406790728,"version":"4.5.0"},"posted":{"date-parts":[[2023,10,19]]},"group-title":"Infectious Diseases (except HIV\/AIDS)","reference-count":55,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,10,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>\n                    The global resurgence of syphilis requires novel prevention strategies. Whole genome sequencing (WGS) of\n                    <jats:italic>Treponema pallidum<\/jats:italic>\n                    (\n                    <jats:italic>TPA<\/jats:italic>\n                    ) using different specimen types is essential for vaccine development.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>\n                    Patients with primary (PS) and secondary (SS) syphilis were recruited in Guangzhou, China. We collected ulcer exudates and blood from PS participants, and skin biopsies and blood from SS participants for\n                    <jats:italic>TPA polA<\/jats:italic>\n                    polymerase chain reaction (PCR); ulcer exudates and blood were also used to isolate\n                    <jats:italic>TPA<\/jats:italic>\n                    strains by rabbit infectivity testing (RIT).\n                    <jats:italic>TPA<\/jats:italic>\n                    WGS was performed on 52 ulcer exudates and biopsy specimens and 25 matched rabbit isolates.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    We enrolled 18 PS and 51 SS participants from December 2019 to March 2022. Among PS participants,\n                    <jats:italic>TPA<\/jats:italic>\n                    DNA was detected in 16 (89%) ulcer exudates and three (17%) blood specimens. Among SS participants,\n                    <jats:italic>TPA<\/jats:italic>\n                    DNA was detected in 50 (98%) skin biopsies and 27 (53%) blood specimens.\n                    <jats:italic>TP<\/jats:italic>\n                    A was isolated from 48 rabbits, with a 71% (12\/17) success rate from ulcer exudates and 69% (36\/52) from SS bloods. Twenty-three matched SS14 clade genomes were virtually identical, while two Nichols clade pairs had discordant\n                    <jats:italic>tprK<\/jats:italic>\n                    sequences. Forty-two of 52 unique\n                    <jats:italic>TPA<\/jats:italic>\n                    genomes clustered in an SS14 East Asia subgroup, while ten fell into two East Asian Nichols subgroups.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>\n                    Our\n                    <jats:italic>TPA<\/jats:italic>\n                    detection rate was high from PS ulcer exudates and SS skin biopsies and over 50% from SS whole blood, with RIT isolation in over two-thirds of samples. Our results support the use of WGS from rabbit isolates to inform vaccine development.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>\n                    We performed\n                    <jats:italic>Treponema pallidum<\/jats:italic>\n                    molecular detection and genome sequencing from multiple specimens collected from early syphilis patients and isolates obtained by rabbit inoculation. Our results support the use of whole genome sequencing from rabbit isolates to inform syphilis vaccine development.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.10.17.23297169","type":"posted-content","created":{"date-parts":[[2023,10,19]],"date-time":"2023-10-19T16:55:11Z","timestamp":1697734511000},"source":"Crossref","is-referenced-by-count":1,"title":["Early syphilis in Guangzhou, China: presentation, molecular detection of\n                  <i>Treponema pallidum<\/i>\n                  , and genomic sequences in clinical specimens and isolates obtained by rabbit infectivity testing"],"prefix":"10.64898","author":[{"given":"Ligang","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohui","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1206-2175","authenticated-orcid":false,"given":"Arlene C.","family":"Se\u00f1a","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heping","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinbo","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peizhen","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rongyi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liuyuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wujian","family":"ke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan C.","family":"Salazar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan B.","family":"Parr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2804-1181","authenticated-orcid":false,"given":"Joseph D.","family":"Tucker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8587-1662","authenticated-orcid":false,"given":"Kelly L.","family":"Hawley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1170-4102","authenticated-orcid":false,"given":"Melissa J.","family":"Caimano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher M.","family":"Hennelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farhang","family":"Aghakanian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feifei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane S.","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. 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Long-term in vitro culture of the syphilis spirochete Treponema pallidum subsp. pallidum . mBio 2018; 9(3).","DOI":"10.1128\/mBio.01153-18"},{"key":"2023102121150484000_2023.10.17.23297169v1.12","doi-asserted-by":"crossref","unstructured":"Edmondson DG , DeLay BD , Kowis LE , Norris SJ . 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