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Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular<jats:italic>C. trachomatis<\/jats:italic>previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia (A\/SA1). No contemporary ocular<jats:italic>C. trachomatis<\/jats:italic>whole genome sequences have been reported from Sudan.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>This study sequenced twenty ocular<jats:italic>C. trachomatis<\/jats:italic>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>All isolates were serovar A and had<jats:italic>tarP<\/jats:italic>and<jats:italic>trpA<\/jats:italic>sequences typical of classical, ocular<jats:italic>C. trachomatis<\/jats:italic>isolates. The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of<jats:italic>C. trachomatis<\/jats:italic>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<jats:italic>C. trachomatis<\/jats:italic>populations, which were focused in two genomic loci (<jats:italic>CTA0172-CTA0173<\/jats:italic>and<jats:italic>CTA0482<\/jats:italic>).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Limited intra-population diversity and geographical clustering of ocular<jats:italic>C. trachomatis<\/jats:italic>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<jats:italic>C. trachomatis<\/jats:italic>growth and transmission in this population.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13071-019-3770-7","type":"journal-article","created":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T13:03:24Z","timestamp":1572872604000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan"],"prefix":"10.1186","volume":"12","author":[{"given":"Abdulazeem Abdulsalam Ibrahim","family":"Alkhidir","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin J.","family":"Holland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wafa Ibrahim","family":"Elhag","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte A.","family":"Williams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judith","family":"Breuer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdah Elfatih","family":"Elemam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khalid Mohamed Khalid","family":"El Hussain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed Elfatih Hussein","family":"Ournasseir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harry","family":"Pickering","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,11,4]]},"reference":[{"key":"3770_CR1","volume-title":"Global Elimination of Blinding Trachoma. 51st World Health Assembly, Geneva, 16 May 1998, Resolution WHA51,","author":"World Health Assembly","year":"1998","unstructured":"World Health Assembly. 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Verbal consent was obtained from community leaders, children or participants\u2019 guardians on their behalf. During the survey, all children with trachomatous inflammation-follicular (TF) and\/or trachomatous inflammation-intense (TI) were treated with a single height-based dose of oral azithromycin in accordance with WHO and national protocols.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"518"}}