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Abstract
Japan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.
Highlights
Japan has had a substantial increase in syphilis cases since 2013
139 Treponema pallidum genomes that satisfied the criteria described in “Methods” were used for phylogenetic analysis: 20 genomes of Treponema pallidum subspecies pallidum (TPA) strains detected in Japan and, in GenBank, 117 genomes of TPA strains and 2 genomes of Treponema pallidum subspecies pertenue (TPE) strains
These 20 TPA strains were from 9 heterosexual males, 6 men who have sex with men (MSM), 4 heterosexual females, and 1 case with missing data on gender and sexual orientation
Summary
Japan has had a substantial increase in syphilis cases since 2013. research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. We elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. Most molecular studies of TPA have been carried out by PCR amplification of several TPA genetic loci[4,5] These have identified some epidemiological features related to the subtype and to the prevalence of macrolide resistance in strains in different countries[6].
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