Phylogenomic_analysis_of_global_Chlamydia_trachomatis_diagnostic_escape_mutants_sequenced_directly_from_clinical_samples. Phylogenomic_analysis_of_global_Chlamydia_trachomatis_diagnostic_escape_mutants_sequenced_directly_from_clinical_samples

Chlamydia is the most common sexually transmitted infection (STI), and is caused by the bacterium Chlamydia trachomatis (Ct). Ct cannot be easily cultured, and STI testing and treatment is largely dependent on molecular diagnostics, e.g. PCR. These molecular diagnostics are vulnerable to changes in the genomic background, leading to mutations that affect primer binding sites and lead to false positives, most famously with the so-called ‘Swedish variant’ that lead to selective of PCR negative Ct before diagnostics were revised. Recently, there has been an increase in the number of molecular diagnostic failures in Scandinavia, and the emergence of the ‘Finnish variant’. Genetic analysis shows that these failures may not be the result of a single mutation, but rather several distinct 23S point mutations. In this study, we will use direct whole genome sequencing to examine the phylogenomic context of examples of Ct with different 23S mutants, in order to establish the ancestry, relatedness, and population size of these outbreaks. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/