Whole-Genome Sequencing of Chlamydia trachomatis Strains B/HAR36 and B/Tunis864

The London School of Hygiene & Tropical Medicine (LSHTM) trachoma group obtained live stocks and genomic DNA from Chlamydia trachomatis (Ct) strains A/2497, A/2497P-, B/HAR36 and C/TW3 via Harlan Caldwell at the Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana. LSHTM provided the Wellcome Trust Sanger Institute (WTSI) genomic DNA from A/2497, B/HAR36 and C/TW3, which underwent full genome sequencing by next generation sequencing and the sequences deposited in the European Nucleotide Archive (ENA) under the following accession numbers (CP002401, ERR189736, and CP006945, respectively). At the start of the EU Horizon-2020 funded TracVac project (2017 – 2022, Grant agreement code: 733373) B/HAR36 was selected for large scale culture to represent serovar B genotypes as part of in vitro and in vivo vaccine studies. Subsequently DNA extracted from these B/HAR36 cultures were subjected to ompA chain-termination sequencing (Sanger sequencing). B/HAR36 labelled ompA sequence was found to be a 100% match for NCBI accession DQ064280 ompA from B/Tunis864 with a lower identity (99%) to NCBI accession DQ064297.1 ompA sequence from B/HAR36. ompA sequence from B/HAR36 whole genome sequence (ERR189736) was extracted and was also match for B/Tunis864. We therefore, obtained original stocks of B/HAR36 and B/Tunis864 from Julius Schachter and Jeanne Moncada at the Francis I Proctor Foundation for research in Ophthalmology, University of California, San Francisco (UCSF) and subjected these to next generation Whole-Genome Sequencing along with B/HAR36 (ERR189736) DNA originally supplied to WTSI. We found that the B/HAR36 ENA sequence (ERR189736) was a match for B/Tunis864. B/HAR36 original stock obtained from UCSF was distinct from B/Tunis864 at the whole genome level and the extracted ompA sequence was a match (100%) for NCBI DQ064297.1 ompA (B/HAR36 ompA).

Keywords

genome sequencing, genome assembly