Abstract
Chlamydia trachomatis infects the urogenital tract (UGT) and eyes. Anatomical tropism is correlated with variation in the major outer membrane protein encoded by ompA. Strains possessing the ocular ompA variants A, B, Ba and C are typically found within the phylogenetically coherent “classical ocular lineage”. However, variants B, Ba and C have also been found within three distinct strains in Australia, all associated with ocular disease in children and outside the classical ocular lineage. CtGEM genotyping is a method for detecting and discriminating ocular strains and also the major phylogenetic lineages. The rationale was facilitation of surveillance to inform responses to C. trachomatis detection in UGT specimens from young children. CtGEM typing is based on high resolution melting analysis (HRMA) of two PCR amplified fragments with high combinatorial resolving power, as defined by computerised comparison of 65 whole genomes. One fragment is from the hypothetical gene defined by Jali-1891 in the C. trachomatis B_Jali20 genome, while the other is from ompA. Twenty combinatorial CtGEM types have been shown to exist, and these encompass unique genotypes for all known ocular strains, and also delineate the TI and T2 major phylogenetic lineages, identify LGV strains and provide additional resolution beyond this. CtGEM typing and Sanger sequencing were compared with 42 C. trachomatis positive clinical specimens, and there were no disjunctions. CtGEM typing is a highly efficient method designed and tested using large scale comparative genomics. It divides C. trachomatis into clinically and biologically meaningful groups, and may have broad application in surveillance.
Highlights
Whole genome-based studies have shown that Chlamydia trachomatis encompasses four major evolutionary lineages [1,2,3,4]
The “lymphogranuloma venereum (LGV)” ompA genotypes L1, L2, and L3 are LGV associated, the urogenital tract (UGT) genotypes D, E, F, G, H, Ia, J, Ja and K are associated with the non-invasive C. trachomatis sexually transmitted infections (STI), and the “ocular” genotypes A, B, Ba and C are associated with trachoma and similar ocular disease exhibiting characteristic “face to face” transmission amongst children
It was found that maximal resolving power from two SNPs was obtained when one of the SNPs was the tri-allelic SNP defined by position 222834 in the C. trachomatis B_Jali20 genome [28] (NC_012686.1), and the other was any of a number of SNPs within ompA
Summary
Whole genome-based studies have shown that Chlamydia trachomatis encompasses four major evolutionary lineages [1,2,3,4]. Of particular relevance to this study, the ocular ompA genotypes B, Ba and C are found in the classical ocular lineage, and in other lineages isolates from northern Australia, from children with ocular disease, and strongly associated with the ocular site [2]. These Australian strains are not within the classical ocular lineage. A very recent large-scale study of global C. trachomatis genome diversity has shown that while the AusBa and AusC clones have as yet been found only in Australia, isolates essentially identical to AusB have been found in Finland and The Netherlands [3]
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