BACKGROUND: Whole-genome sequencing (WGS) of Treponema pallidum subspecies pallidum (TPA) has been constrained by the lack of in vitro cultivation methods for isolating spirochetes from patient samples. METHODS: We built upon recently developed enrichment methods to sequence TPA directly from primary syphilis chancre swabs collected in Guangzhou, China. RESULTS: By combining parallel, pooled whole-genome amplification with hybrid selection, we generated high-quality genomes from 4 of 8 chancre-swab samples and 2 of 2 rabbit-passaged isolates, all subjected to challenging storage conditions. CONCLUSIONS: This approach enabled the first WGS of Chinese samples without rabbit passage and provided insights into TPA genetic diversity in China.

Curriculum in Genetics and Molecular Biology School of Medicine University of North Carolina Chapel Hill North Carolina USA

Department of Biology Faculty of Medicine Masaryk University Brno Czech Republic

Department of Epidemiology Gillings School of Global Public Health University of North Carolina Chapel Hill North Carolina USA

Departments of Genetics and Genome Sciences and Immunology UConn Health Farmington Connecticut USA

Departments of Medicine Pediatrics and Molecular Biology and Biophysics UConn Health Farmington Connecticut USA

Dermatology Hospital Southern Medical University Guangzhou China

Division of Infectious Diseases and Department of Pediatrics Connecticut Children's Medical Center Hartford Connecticut USA

Division of Infectious Diseases Department of Medicine University of North Carolina Chapel Hill North Carolina USA

Faculty of Infectious and Tropical Diseases London School of Hygiene and Tropical Medicine London United Kingdom

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Majority of Treponema pallidum ssp. pallidum MLST allelic profiles in the Czech Republic (2004-2022) belong to two SS14-like clusters