A novel Treponema pallidum subsp. pallidum strain associated with a painful oral lesion is a member of a potentially emerging Nichols-related subgroup

Abstract

Abstract Background Early syphilitic lesions are typically painless; however, several recent case studies have included patients with tender lesions and no evidence of concurrent infections. Here we present the manifestations and serological and molecular findings of a patient from New York State with a painful tongue lesion. Methods The diagnosis of syphilis was based on a combination of physical examination, serologic, pathologic, and immunohistochemical findings. DNA obtained from a formalin fixed paraffin embedded (FFPE) biopsy was used to characterize the infecting pathogen using PCR, multilocus sequence typing (MLST), and whole genome sequencing (WGS) methods. Results PCR and MLST of the biopsy specimen confirmed infection with Treponema pallidum subsp. pallidum (T. pallidum) of the Nichols cluster. WGS analysis of this strain (herein called NYMC01) showed that it contained 17 unique single nucleotide variations and 4 more complex genetic differences; this novel genotype matched only two specimens, both from a patient in Seattle, Washington, U.S.A. The presence of this rare genotype in two geographically distinct locations suggests the potential emergence and spread of a new subgroup of the Nichols cluster. Conclusions To our knowledge, this is the first genomic sequence obtained from a T. pallidum strain linked to a painful lesion, and the third description of whole genome sequencing of T. pallidum from FFPE tissue. Analysis of additional specimens may reveal that the NYMC01-related genotype represents an emerging T. pallidum subgroup and may also aid in determining whether the painful clinical presentation of primary syphilis is related to specific T. pallidum genotypes.