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Volume 32, Number 4—April 2026

Dispatch

Whole-Genome Analysis of Treponema pallidum Subspecies endemicum among Men Who Have Sex with Men, Japan, 2020–2023

Yuki OhamaComments to Author , Kazuo Imai, Yuto Kotaka, Kenichi Lee, Ichiro Itoda, Shu-ichi Nakayama, Makoto Ohnishi, and Yukihiro Akeda
Author affiliation: National Institute of Infectious Diseases, Tokyo, Japan (Y. Ohama, Y. Kotaka, K. Lee, S. Nakayama, M. Ohnishi, Y. Akeda); Saitama Medical University, Saitama, Japan (K. Imai); Tokyo Metropolitan University, Tokyo (Y. Kotaka); Shirakaba Clinic, Tokyo (I. Itoda)

Main Article

Figure

Phylogenetic analysis of isolates from a study of whole-genome analysis of Treponema pallidum subspecies endemicum among men who have sex with men, Japan, 2020–2023. Open reading frames annotated from de novo assembled contigs using Bakta version 1.7.0 (https://bakta.computational.bio), and corresponding GFF3 annotation files processed with Panaroo version 1.2.3 (https://zenodo.org/records/3945497) to define core genomes across isolates. Multiple alignments of core gene sequences generated by Panaroo were used for phylogenetic reconstruction. T. pallidum subsp. pallidum SS14 (GenBank accession no. NC_021508) was used as a reference strain. IQ-TREE version 2.2.0 (http://www.iqtree.org) was used to infer maximum-likelihood phylogenies, incorporating 1,000 ultrafast bootstrap replicates to assess nodal support. Phylogenetic tree was visualized by using Interactive Tree of Life (iTOL; https://itol.embl.de). The T. pallidum subsp. endemicum strains isolated in Japan formed a clade distinct from classic endemic strains, including Iraq B and strains from Cuba (C77 and C279). Scale bar indicates nucleotide substitutions per site.

Figure. Phylogenetic analysis of isolates from a study of whole-genome analysis of Treponema pallidum subspecies endemicum among men who have sex with men, Japan, 2020–2023. Open reading frames annotated from de novo assembled contigs using Bakta version 1.7.0 (https://bakta.computational.bio), and corresponding GFF3 annotation files processed with Panaroo version 1.2.3 (https://zenodo.org/records/3945497) to define core genomes across isolates. Multiple alignments of core gene sequences generated by Panaroo were used for phylogenetic reconstruction. T. pallidum subsp. pallidum SS14 (GenBank accession no. NC_021508) was used as a reference strain. IQ-TREE version 2.2.0 (http://www.iqtree.org) was used to infer maximum-likelihood phylogenies, incorporating 1,000 ultrafast bootstrap replicates to assess nodal support. Phylogenetic tree was visualized by using Interactive Tree of Life (iTOL; https://itol.embl.de). The T. pallidum subsp. endemicum strains isolated in Japan formed a clade distinct from classic endemic strains, including Iraq B and strains from Cuba (C77 and C279). Scale bar indicates nucleotide substitutions per site.

Main Article

Page created: March 20, 2026
Page updated: April 15, 2026
Page reviewed: April 15, 2026
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