_GeneSyS__Genome_sequencing_syphilis_directly_from_clinical_samples_____

Syphilis is a global health problem with an estimated 12 million incident cases globally each year. It is caused by Treponema pallidum sub-species pallidum (TPP), an uncultivable bacterium of the family Spirochaeticea, with a genome size of 1.14Mbp with open reading frames with approximately 1090 genes coding for 1041 proteins. Despite its small genome size, TPP has a very complicated structure and metabolic capability. Despite being one of the first infections to be successfully treated with antibiotics, what optimal syphilis treatment is remains contraversial, as TPP cannot be cultured in vitro on standard culture media or in tissue culture, hence making it very difficult to define cure or to determine antibiotic sensitivity. The only method of labarotory culture is through passage in rabbit testes. The complete genome for TPP was first sequenced in 1998 from the reference Nichols strain. Several whole genome sequences of TPP have been reported since from reference strains and clinical isolates passaged through rabbit testes. Little variation in genomic structure has been described, despite widely different clinical presentations. The lack of variation might be attributable to adaptation within the rabbit host. We aim to sequence the TPP genome directly from clinical swab specimens in this feasibility study to overcome the possibilty of host driven adaptation of the TPP genome. The overall aim is to perform whole genome sequencing of Treponema pallidum sub-species pallidum from DNA extracts from swab samples from genital ulcers.