{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:22:04Z","timestamp":1787962924136,"version":"build-2784847793"},"posted":{"date-parts":[[2023,1,26]]},"group-title":"Microbiology","reference-count":46,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,1,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  <jats:italic>Chlamydia trachomatis<\/jats:italic>\n                  , a gram-negative obligate intracellular bacterium, commonly causes sexually transmitted infections (STIs). Little is known about\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  transmission within the host, which is important for understanding disease epidemiology and progression. We used RNA-bait enrichment and whole-genome sequencing to compare rectal, vaginal and endocervical samples collected at the same time from 26 study participants who attended Fijian Ministry of Health and Medical Services clinics and tested positive for\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  at each anatomic site. The 78\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  genomes from participants were from two major clades of the\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  phylogeny (the \u201cprevalent urogenital and anorecta\u201dl clade and \u201cnon-prevalent urogenital and anorectal\u201d clade). For 21 participants, genome sequences were almost identical in each anatomic site. For the other five participants, two distinct\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  strains were present in different sites; in two cases, the vaginal sample was a mixture of strains. The absence of large numbers of fixed SNPs between\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  strains within many of the participants could indicate recent acquisition of infection prior to the clinic visit without sufficient time to accumulate significant variation in the different body sites. This model suggests that many\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  infections may be resolved relatively quickly in the Fijian population, possibly reflecting common prescription or over-the-counter antibiotics usage.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Importance<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Chlamydia trachomatis<\/jats:italic>\n                    is a bacterial pathogen that causes millions of sexually transmitted infections (STIs) annually across the globe. Because\n                    <jats:italic>C. trachomatis<\/jats:italic>\n                    lives inside human cells, it has historically been hard to study. We know little about how the bacterium spreads between body sites. Here, samples from 26 study participants who had simultaneous infections in their vagina, rectum and endocervix were genetically analyzed using an improved method to extract\n                    <jats:italic>C. trachomatis<\/jats:italic>\n                    DNA directly from clinical samples for genome sequencing. By analyzing patterns of mutations in the genomes, we found that 21 participants shared very similar\n                    <jats:italic>C. trachomatis<\/jats:italic>\n                    strains in all three anatomic sites, suggesting recent infection and spread. For five participants two\n                    <jats:italic>C. trachomatis<\/jats:italic>\n                    strains were evident, indicating multiple infections. This study is significant in that improved enrichment methods for genome sequencing provides robust data to genetically trace patterns of\n                    <jats:italic>C. trachomatis<\/jats:italic>\n                    infection and transmission within an individual for epidemiologic and pathogenesis interrogations.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.01.25.525576","type":"posted-content","created":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T20:15:16Z","timestamp":1674764116000},"source":"Crossref","is-referenced-by-count":4,"title":["Patterns of within-host spread of\n                  <i>Chlamydia trachomatis<\/i>\n                  between vagina, endocervix and rectum revealed by comparative genomic analysis"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0697-2487","authenticated-orcid":false,"given":"Sandeep J.","family":"Joseph","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4469-7925","authenticated-orcid":false,"given":"Sankhya","family":"Bommana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noa","family":"Ziklo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Kama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4490-1746","authenticated-orcid":false,"given":"Deborah","family":"Dean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8966-9680","authenticated-orcid":false,"given":"Timothy D.","family":"Read","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2023012717351733000_2023.01.25.525576v1.1","unstructured":"World Health Organization. 2020. Sexually Transmitted Infections (STIs) Key facts. http:\/\/www.who.int\/mediacentre\/factsheets\/fs110\/en\/."},{"key":"2023012717351733000_2023.01.25.525576v1.2","unstructured":"Centers for Disease Control and Prevention, Department of Health and Human Services. 2021. Sexually Transmitted Diseases Surveillance 2019."},{"key":"2023012717351733000_2023.01.25.525576v1.3","unstructured":"Batteiger BE . 2020. Chlamydia trachomatis, p.. In Bennett, J , Dolin, R , Blaser, MJ (eds.), Mandell, Douglas, and Bennett\u2019s Principles and Practice of Infectious Diseases. 9th Edition. Elsevier."},{"key":"2023012717351733000_2023.01.25.525576v1.4","doi-asserted-by":"publisher","DOI":"10.1097\/OLQ.0b013e318286bb53"},{"key":"2023012717351733000_2023.01.25.525576v1.5","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1098-0997(2000)8:2<83::AID-IDOG4>3.0.CO;2-4"},{"key":"2023012717351733000_2023.01.25.525576v1.6","doi-asserted-by":"publisher","DOI":"10.1086\/652395"},{"key":"2023012717351733000_2023.01.25.525576v1.7","doi-asserted-by":"publisher","DOI":"10.1155\/2016\/5758387"},{"key":"2023012717351733000_2023.01.25.525576v1.8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0140297"},{"key":"2023012717351733000_2023.01.25.525576v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/civ756"},{"key":"2023012717351733000_2023.01.25.525576v1.10","doi-asserted-by":"crossref","unstructured":"Chandra NL , Broad C , Folkard K , Town K , Harding-Esch EM , Woodhall SC , Saunders JM , Sadiq ST , Dunbar JK . 2018. Detection of Chlamydia trachomatis in rectal specimens in women and its association with anal intercourse: a systematic review and meta-analysis. Sex Transm Infect https:\/\/doi.org\/10.1136\/sextrans-2017-053161.","DOI":"10.1136\/sextrans-2017-053161"},{"key":"2023012717351733000_2023.01.25.525576v1.11","doi-asserted-by":"publisher","DOI":"10.1258\/ijsa.2011.010490"},{"key":"2023012717351733000_2023.01.25.525576v1.12","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1093\/jac\/dkx392","article-title":"Chlamydia trachomatis antimicrobial susceptibility in colorectal and endocervical cells","volume":"73","year":"2018","journal-title":"J Antimicrob Chemother"},{"key":"2023012717351733000_2023.01.25.525576v1.13","doi-asserted-by":"publisher","DOI":"10.1177\/0956462415618837"},{"key":"2023012717351733000_2023.01.25.525576v1.14","doi-asserted-by":"publisher","DOI":"10.1097\/OLQ.0000000000000088"},{"key":"2023012717351733000_2023.01.25.525576v1.15","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cix243"},{"key":"2023012717351733000_2023.01.25.525576v1.16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0081236"},{"key":"2023012717351733000_2023.01.25.525576v1.17","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciu220"},{"key":"2023012717351733000_2023.01.25.525576v1.18","doi-asserted-by":"crossref","first-page":"e0008022","DOI":"10.1371\/journal.pntd.0008022","article-title":"Hyperendemic Chlamydia trachomatis sexually transmitted infections among females represent a high burden of asymptomatic disease and health disparity among Pacific Islanders in Fiji","volume":"14","year":"2020","journal-title":"PLoS Negl Trop Dis"},{"key":"2023012717351733000_2023.01.25.525576v1.19","doi-asserted-by":"crossref","unstructured":"Bowden KE , Joseph SJ , Cartee JC , Ziklo N , Danavall D , Raphael BH , Read TD , Dean D . 2021. 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R: A language and environment for statistical computing. https:\/\/www.R-project.org\/."}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.01.25.525576","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T04:11:26Z","timestamp":1768450286000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.01.25.525576"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,26]]},"references-count":46,"URL":"https:\/\/doi.org\/10.1101\/2023.01.25.525576","relation":{},"subject":[],"published":{"date-parts":[[2023,1,26]]},"subtype":"preprint"}}