{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T03:34:01Z","timestamp":1791948841849,"version":"4.3.4"},"reference-count":160,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,5,23]],"date-time":"2023-05-23T00:00:00Z","timestamp":1684800000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>The genus <jats:italic>Chlamydia<\/jats:italic> contains important obligate intracellular bacterial pathogens to humans and animals, including <jats:italic>C. trachomatis<\/jats:italic> and <jats:italic>C. pneumoniae<\/jats:italic>. Since 1998, when the first <jats:italic>Chlamydia<\/jats:italic> genome was published, our understanding of how these microbes interact, evolved and adapted to different intracellular host environments has been transformed due to the expansion of chlamydial genomes. This review explores the current state of knowledge in <jats:italic>Chlamydia<\/jats:italic> genomics and how whole genome sequencing has revolutionised our understanding of <jats:italic>Chlamydia<\/jats:italic> virulence, evolution, and phylogeny over the past two and a half decades. This review will also highlight developments in multi-omics and other approaches that have complemented whole genome sequencing to advance knowledge of <jats:italic>Chlamydia<\/jats:italic> pathogenesis and future directions for chlamydial genomics.<\/jats:p>","DOI":"10.3389\/fcimb.2023.1178736","type":"journal-article","created":{"date-parts":[[2023,5,23]],"date-time":"2023-05-23T05:09:09Z","timestamp":1684818549000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":44,"title":["Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of\u00a0chlamydial virulence, evolution, and phylogeny"],"prefix":"10.3389","volume":"13","author":[{"given":"Laurence Don Wai","family":"Luu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasilli","family":"Kasimov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Phillips","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garry S. 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