{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T14:36:06Z","timestamp":1787236566356,"version":"build-2736575974"},"reference-count":36,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T00:00:00Z","timestamp":1764633600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T00:00:00Z","timestamp":1764633600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["23fk0108676, 24fk0108676"],"award-info":[{"award-number":["23fk0108676, 24fk0108676"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,12,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Molecular surveillance aimed at identifying the subspecies and lineages of\n                      <jats:italic toggle=\"yes\">Treponema pallidum<\/jats:italic>\n                      is important. Conventional molecular\n                        methods for genotyping are effective but are also time-consuming and costly.\n                        This study aimed to develop and evaluate a novel loop-mediated isothermal\n                        amplification (LAMP) method using quenching probes to quickly distinguish\n                      <jats:italic toggle=\"yes\">T. pallidum<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">pallidum<\/jats:italic>\n                      lineages\n                        (Nichols, SS14\u03a9-A, SS14\u03a9-B 1A, and SS14-East Asia) and\n                      <jats:italic toggle=\"yes\">T. pallidum<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">endemicum<\/jats:italic>\n                      circulating in East Asia. We developed novel LAMP assays for genotyping the\n                      <jats:italic toggle=\"yes\">tp0705<\/jats:italic>\n                      (amino acid variants of 506, 625, and 708) and\n                      <jats:italic toggle=\"yes\">tp0548<\/jats:italic>\n                      genes (a 9 bp insertion region). The LAMP assays\n                        were used to genotype 133 clinical samples (Nichols,\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 9;\n                        SS14\u03a9-A,\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 7; SS14\u03a9-B 1A,\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 2; SS14-East Asia,\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 110; and\n                      <jats:italic toggle=\"yes\">T. pallidum<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">endemicum<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 5) collected from adult patients diagnosed with\n                        syphilis in Japan. The genotyping results of the LAMP assays were compared\n                        with the results from Sanger or whole-genome sequencing. The lower detection\n                        limit of the LAMP assays for\n                      <jats:italic toggle=\"yes\">tp0705<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">tp0548<\/jats:italic>\n                      genotyping was 20 DNA copies\/reaction. Of the\n                        133 samples analyzed, the genotypes, lineages, and subspecies of\n                      <jats:italic toggle=\"yes\">T.\n                            pallidum<\/jats:italic>\n                      were identified in 129 (97.0%) samples by the LAMP\n                        assays. The genotyping results of the LAMP assays were completely consistent\n                        with those of Sanger and whole-genome sequencing. Our novel LAMP genotyping\n                        assays can rapidly and easily discriminate the lineages and subspecies of\n                      <jats:italic toggle=\"yes\">T. pallidum<\/jats:italic>\n                      circulating in East Asia. This method will\n                        contribute to the epidemiological surveillance of\n                      <jats:italic toggle=\"yes\">T.\n                            pallidum<\/jats:italic>\n                      in East Asia.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Syphilis remains a significant global public health concern. Molecular\n                        surveillance is essential for understanding the transmission dynamics and\n                        spread of various\n                      <jats:italic toggle=\"yes\">Treponema pallidum<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">pallidum<\/jats:italic>\n                      lineages, including emerging strains such as\n                      <jats:italic toggle=\"yes\">Treponema pallidum<\/jats:italic>\n                      subsp.\n                      <jats:italic toggle=\"yes\">endemicum<\/jats:italic>\n                      (TEN). However, conventional genotyping methods like multi-locus sequence\n                        typing and whole-genome sequencing are costly, time-consuming, and require\n                        specialized equipment and expertise. In this study, we developed a novel\n                        loop-mediated isothermal amplification assay with quenching probes that\n                        enables rapid, accurate, and low-cost identification of major\n                      <jats:italic toggle=\"yes\">T.\n                            pallidum<\/jats:italic>\n                      lineages and subspecies. Our method demonstrated high\n                        sensitivity and specificity using clinical specimens and successfully\n                        distinguished among Nichols, SS14 variants, and TEN. This assay is well\n                        suited for large-scale epidemiological studies and may support more\n                        effective and timely public health responses to the rising incidence of\n                        syphilis in East Asia and beyond.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01565-25","type":"journal-article","created":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T13:15:02Z","timestamp":1761830102000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Loop-mediated isothermal amplification assays for the rapid                    discrimination of\n                    <i>Treponema pallidum<\/i>\n                    lineages and                    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