Abstract
BackgroundTrachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular C. trachomatis previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia (A/SA1). No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan.MethodsThis study sequenced twenty ocular C. trachomatis isolates to improve understanding of pathogen diversity in North-East Africa and examine for genomic variation specific to Sudan, possibly related to the persistence of trachoma in surveyed communities. High quality, whole genome sequences were obtained from 12/20 isolates.ResultsAll isolates were serovar A and had tarP and trpA sequences typical of classical, ocular C. trachomatis isolates. The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of C. trachomatis phylogeny distinct from geographically disparate ocular isolates, with little intra-population diversity. We found 333 SNPs that were conserved in Sudanese ocular isolates but rare compared to other ocular C. trachomatis populations, which were focused in two genomic loci (CTA0172-CTA0173 and CTA0482).ConclusionsLimited intra-population diversity and geographical clustering of ocular C. trachomatis suggests minimal transmission between and slow diversification within trachoma-endemic communities. However, diversity may have been higher pre-treatment in these communities. Over-representation of Sudan-specific SNPs in three genes suggests they may have an impact on C. trachomatis growth and transmission in this population.
Highlights
Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide
In 2018, we published a study from Bijagos Islands, Guinea-Bissau that used a genome-wide association study of 81 ocular C. trachomatis isolates to identify genomic markers of disease severity in trachoma [25]; this study suggested there is C. trachomatis genomic diversity within populations and that it may be linked to clinical outcomes
This study found 333 alleles conserved within Sudan and rare within the global ocular C. trachomatis population were focussed in two distinct genomic regions
Summary
Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan. Chlamydia trachomatis is one of the most common sexually transmitted infections worldwide and the leading infectious cause of blindness. Reduced cost and improvements in technique [12,13,14] have seen a significant increase in whole-genome sequencing (WGS) of C. trachomatis; most studies have not investigated the relationship between sequence variation and clinical outcomes [15,16,17,18,19,20,21]. In 2018, we published a study from Bijagos Islands, Guinea-Bissau that used a genome-wide association study of 81 ocular C. trachomatis isolates to identify genomic markers of disease severity in trachoma [25]; this study suggested there is C. trachomatis genomic diversity within populations and that it may be linked to clinical outcomes
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