Nextstrain TrepoGen is a reproducible Nextstrain workflow for tracking bacterial diversity at both genome- and gene-level. It integrates genetic variants and sequence data with manually curated metadata, including protein topology predictions, to produce interactive phylogenies and automated per-feature typing for downstream analyses.
Further background on Nextstrain can be found in the Exploring interactive phylogenies with Auspice tutorial and the Nextstrain Glossary.
Syphilis is a resurging global health threat caused by Treponema pallidum ssp. pallidum, with additional disease burden from the closely related subspecies pertenue and endemicum, the causative agents of yaws and bejel, respectively. By 2025 whole genome sequencing data for more than 3,000 T. pallidum strains were available in the NCBI Sequence Read Archive. However, more than 80% of these lack publicly available genome assemblies and, more critically, systematic annotation. This severely limits their utility for molecular epidemiology, resistance surveillance, and vaccine development.
We aim at democratizing access to T. pallidum genomic diversity data by developing and maintaining unified, community-facing Nextstrain datasets for epidemiological surveillance, comparative evolutionary analysis and facilitated data sharing; with a special emphasis on tracking outer membrane protein (OMP) diversity relevant for vaccine design.
Our Nextstrain datasets are currently private. We’re actively preparing to release it to the public soon and will update this repository with more details once available.
Further information on the details of Nextstrain-TrepoGen can be found in this repositories Wiki.
This project receives funding To support the development of a broadly effective syphilis vaccine (INV-072205) from the Gates Foundation. We thank the authors, originators and submitting laboratories of the genetic sequences and metadata for providing their work and are currently working on a comprehensive list of data provenance. Moreover, we would like to thank the Nextstrain community and the Nextstrain team for the development of the augur/auspice ecosystem and their valuable support for this project.