{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T15:41:08Z","timestamp":1776872468219,"version":"3.51.2"},"reference-count":114,"publisher":"Microbiology Society","issue":"3","license":[{"start":{"date-parts":[[2024,3,6]],"date-time":"2024-03-06T00:00:00Z","timestamp":1709683200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Austrian Science Fund","award":["J-4608"],"award-info":[{"award-number":["J-4608"]}]},{"name":"Medical Research Council","award":["G9826361\/ ID48103"],"award-info":[{"award-number":["G9826361\/ ID48103"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["079246\/Z\/06"],"award-info":[{"award-number":["079246\/Z\/06"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"crossref","award":["733373"],"award-info":[{"award-number":["733373"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,6]]},"abstract":"<jats:p>\n                    Trachoma, a neglected tropical disease caused by\n                    <jats:italic>Chlamydia trachomatis<\/jats:italic>\n                    (Ct) serovars A\u2013C, is the leading infectious cause of blindness worldwide. Africa bears the highest burden, accounting for over 86\u200a% of global trachoma cases. We investigated Ct serovar A (SvA) and B (SvB) whole genome sequences prior to the induction of mass antibiotic drug administration in The Gambia. Here, we explore the factors contributing to Ct strain diversification and the implications for Ct evolution within the context of ocular infection. A cohort study in 2002\u20132003 collected ocular swabs across nine Gambian villages during a 6\u2009month follow-up study. To explore the genetic diversity of Ct within and between individuals, we conducted whole-genome sequencing (WGS) on a limited number (\n                    <jats:italic>n<\/jats:italic>\n                    =43) of Ct-positive samples with an\n                    <jats:italic>omc<\/jats:italic>\n                    B load \u226510 from four villages. WGS was performed using target enrichment with SureSelect and Illumina paired-end sequencing. Out of 43 WGS samples, 41 provided sufficient quality for further analysis.\n                    <jats:italic>omp<\/jats:italic>\n                    A analysis revealed that 11\u2009samples had highest identity to\n                    <jats:italic>omp<\/jats:italic>\n                    A from strain A\/HAR13 (NC_007429) and 30 had highest identity to\n                    <jats:italic>omp<\/jats:italic>\n                    A from strain B\/Jali20 (NC_012686). While SvB genome sequences formed two distinct village-driven subclades, the heterogeneity of SvA sequences led to the formation of many individual branches within the Gambian SvA subclade. Comparing the Gambian SvA and SvB sequences with their reference strains, Ct A\/HAR13 and Ct B\/Jali20, indicated an single nucleotide polymorphism accumulation rate of 2.4\u00d710\n                    <jats:sup>\u22125<\/jats:sup>\n                    per site per year for the Gambian SvA and 1.3\u00d710\n                    <jats:sup>\u22125<\/jats:sup>\n                    per site per year for SvB variants (\n                    <jats:italic>P<\/jats:italic>\n                    &lt;0.0001). Variant calling resulted in a total of 1371 single nucleotide variants (SNVs) with a frequency &gt;25\u200a% in SvA sequences, and 438 SNVs in SvB sequences. Of note, in SvA variants, highest evolutionary pressure was recorded on genes responsible for host cell modulation and intracellular survival mechanisms, whereas in SvB variants this pressure was mainly on genes essential for DNA replication\/repair mechanisms and protein synthesis. A comparison of the sequences between observed separate infection events (4\u201320\u2009weeks between infections) suggested that the majority of the variations accumulated in genes responsible for host\u2013pathogen interaction such as CTA_0166 (phospholipase D-like protein), CTA_0498 (TarP) and CTA_0948 (deubiquitinase). This comparison of Ct SvA and SvB variants within a trachoma endemic population focused on their local evolutionary adaptation. We found a different variation accumulation pattern in the Gambian SvA chromosomal genes compared with SvB, hinting at the potential of Ct serovar-specific variation in diversification and evolutionary fitness. These findings may have implications for optimizing trachoma control and prevention strategies.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001210","type":"journal-article","created":{"date-parts":[[2024,3,6]],"date-time":"2024-03-06T09:16:49Z","timestamp":1709716609000},"source":"Crossref","is-referenced-by-count":6,"title":["Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages"],"prefix":"10.1099","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1019-6572","authenticated-orcid":false,"given":"Ehsan","family":"Ghasemian","sequence":"first","affiliation":[{"name":"Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nkoyo","family":"Faal","sequence":"additional","affiliation":[{"name":"Medical Research Council Unit The Gambia at London School of Hygiene and 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