OBJECTIVE: Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget.10154 ) described a new "phylogenetic group" (called Lineage 2) among Chinese TPA strains. This lineage exhibited a "mosaic genomic structure" of Nichols-like and SS14-like lineages. RESULTS: We reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identified: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains.

CEITEC Central European Institute of Technology Masaryk University Brno Czech Republic

Center for Bioinformatics University of Tübingen Tübingen Germany

CIBER Epidemiologia y Salud Pública Valencia Spain

Department of Biology Faculty of Medicine Masaryk University Kamenice 5 Building A6 625 00 Brno Czech Republic

Institute for Integrative Systems Biology Universidad de Valencia CSIC Valencia Spain

National Centre for Biomolecular Research Masaryk University Brno Czech Republic

Unidad Mixta Infección y Salud Pública FISABIO Universidad de Valencia Valencia Spain

Zurich Institute of Forensic Medicine University of Zurich Zurich Switzerland

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