{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T02:48:46Z","timestamp":1767926926954,"version":"3.49.0"},"reference-count":41,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2023,4,8]],"date-time":"2023-04-08T00:00:00Z","timestamp":1680912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PI17\/01886"],"award-info":[{"award-number":["PI17\/01886"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union","award":["PI17\/01886"],"award-info":[{"award-number":["PI17\/01886"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Chlamydia trachomatis infection is an important public health problem. Our objective was to assess the dynamics of the transmission of this infection, analysing the distribution of circulating ompA genotypes and multilocus sequence types of C. trachomatis in Spain as a function of clinical and epidemiological variables. During 2018 and 2019, we genetically characterized C. trachomatis in tertiary hospitals in six areas in Spain (Asturias, Barcelona, Gipuzkoa, Mallorca, Seville and Zaragoza), with a catchment population of 3.050 million people. Genotypes and sequence types were obtained using polymerase chain reaction techniques that amplify a fragment of the ompA gene, and five highly variable genes (hctB, CT058, CT144, CT172 and pbpB), respectively. Amplicons were sequenced and phylogenetic analysis was conducted. We obtained genotypes in 636\/698 cases (91.1%). Overall and by area, genotype E was the most common (35%). Stratifying by sex, genotypes D and G were more common among men, and genotypes F and I among women (p &lt; 0.05). Genotypes D, G and J were more common in men who have sex with men (MSM) than in men who have sex with women (MSW), in whom the most common genotypes were E and F. The diversity index was higher in sequence typing (0.981) than in genotyping (0.791), and the most common sequence types were ST52 and ST108 in MSM, and ST30, ST148, ST276 and ST327 in MSW. Differences in genotype distribution between geographical areas were attributable to differences in population characteristics. The transmission dynamics varied with sexual behaviour: the predominant genotypes and most frequent sequence types found in MSM were different to those detected in MSW and women.<\/jats:p>","DOI":"10.3390\/ijms24086941","type":"journal-article","created":{"date-parts":[[2023,4,10]],"date-time":"2023-04-10T03:49:29Z","timestamp":1681098569000},"page":"6941","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Genetic Characterization of Non-Lymphogranuloma venereum\u00a0Chlamydia trachomatis Indicates Distinct Infection Transmission Networks in Spain"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4196-5557","authenticated-orcid":false,"given":"Luis","family":"Pi\u00f1eiro","sequence":"first","affiliation":[{"name":"Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, 20014 San Sebastian, Spain"},{"name":"Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4228-7041","authenticated-orcid":false,"given":"Laura","family":"Villa","sequence":"additional","affiliation":[{"name":"Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain"},{"name":"Microbiology Department, Central University Hospital of Asturias, 33011 Oviedo, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paula","family":"Salmer\u00f3n","sequence":"additional","affiliation":[{"name":"Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain"},{"name":"Microbiology Department, Vall d\u2019Hebr\u00f3n University Hospital, 08035 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Dolores","family":"Maci\u00e1","sequence":"additional","affiliation":[{"name":"Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain"},{"name":"Microbiology Department, Son Espases University Hospital, 07120 Palma de Mallorca, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luis","family":"Otero","sequence":"additional","affiliation":[{"name":"Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain"},{"name":"Microbiology Department, Cabue\u00f1es University Hospital, 33394 Gij\u00f3n, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mart\u00ed","family":"Vall-Mayans","sequence":"additional","affiliation":[{"name":"Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain"},{"name":"Vall\u2019Hebron-Drassanes STI Unit, Infectious Diseases Department, Vall d\u2019Hebr\u00f3n University Hospital, 08035 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana","family":"Milagro","sequence":"additional","affiliation":[{"name":"Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain"},{"name":"Microbiology Department, Miguel Servet University Hospital, 50009 Zaragoza, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel","family":"Bernal","sequence":"additional","affiliation":[{"name":"Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain"},{"name":"Infectious Diseases and Microbiology Unit, Valme University Hospital, 41014 Seville, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6628-8305","authenticated-orcid":false,"given":"Ayla","family":"Manzanal","sequence":"additional","affiliation":[{"name":"Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, 20014 San Sebastian, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"I\u00f1igo","family":"Ansa","sequence":"additional","affiliation":[{"name":"Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, 20014 San Sebastian, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gustavo","family":"Cilla","sequence":"additional","affiliation":[{"name":"Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, 20014 San Sebastian, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,4,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"548","DOI":"10.2471\/BLT.18.228486","article-title":"Chlamydia, gonorrhoea, trichomoniasis and syphilis: Global prevalence and incidence estimates 2016","volume":"97","author":"Rowley","year":"2019","journal-title":"Bull. World Health Organ."},{"key":"ref_2","unstructured":"European Centre for Disease Prevention and Control (2016). Guidance on Chlamydia Control in Europe\u20132015."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Bom, R.J., Van Der Helm, J.J., Schim Van Der Loeff, M.F., Van Rooijen, M.S., Heijman, T., Matser, A., De Vries, H.J., and Bruisten, S.M. (2013). Distinct transmission networks of Chlamydia trachomatis in men who have sex with men and heterosexual adults in Amsterdam, The Netherlands. PLoS ONE., 8.","DOI":"10.1371\/journal.pone.0053869"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1101\/gr.212647.116","article-title":"Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion","volume":"27","author":"Hadfield","year":"2017","journal-title":"Genome Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2844","DOI":"10.1128\/JCM.00128-11","article-title":"Evaluation of high-resolution typing methods for Chlamydia trachomatis in samples from heterosexual couples","volume":"49","author":"Bom","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/ng.2214","article-title":"Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing","volume":"44","author":"Harris","year":"2012","journal-title":"Nat. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1128\/IAI.71.3.1200-1208.2003","article-title":"Polymorphic membrane protein H has evolved in parallel with the three disease-causing groups of Chlamydia trachomatis","volume":"71","author":"Stothard","year":"2003","journal-title":"Infect. Immun."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1172\/JCI17993","article-title":"Polymorphisms in Chlamydia trachomatis tryptophan synthase genes differentiate between genital and ocular isolates","volume":"111","author":"Caldwell","year":"2003","journal-title":"J. Clin. Invest."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"910E5","DOI":"10.1016\/j.cmi.2018.01.025","article-title":"Chlamydia trachomatis genotypes A and B from urogenital specimens of patients in Spain: Molecular characterization","volume":"24","author":"Isaksson","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_10","unstructured":"(2023, April 04). Unidad de Vigilancia de VIH, ITS y Hepatitis B y C. Vigilancia Epidemiol\u00f3gica de Las Infecciones de Transmisi\u00f3n Sexual, 2019. Centro Nacional de Epidemiolog\u00eda, Instituto de Salud Carlos III\/Plan Nacional Sobre el Sida, Direcci\u00f3n General de Salud P\u00fablica. Available online: https:\/\/www.isciii.es\/QueHacemos\/Servicios\/VigilanciaSaludPublicaRENAVE\/EnfermedadesTransmisibles\/Documents\/archivos%20A-Z\/SIFILIS\/Vigilancia_ITS_1995_2021.pdf."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"185","DOI":"10.2340\/00015555-1234","article-title":"Absence of Swedish new variant Chlamydia trachomatis (nvCT) and C. trachomatis genotype distribution in Gipuzkoa, Spain, 2009-2010","volume":"92","author":"Unemo","year":"2012","journal-title":"Acta Derm. Venereol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e002330","DOI":"10.1136\/bmjopen-2012-002330","article-title":"Genotyping Chlamydia trachomatis strains among men who have sex with men from a Northern Spain region: A cohort study","volume":"3","author":"Mejuto","year":"2013","journal-title":"BMJ Open"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1007\/s15010-014-0665-6","article-title":"Minimum spread of the new Swedish variant of Chlamydia trachomatis and distribution of C. trachomatis ompA genotypes in three geographically distant areas of Spain, 2011\u20132012","volume":"42","author":"Bernal","year":"2014","journal-title":"Infection"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.eimc.2008.12.012","article-title":"Genotipado de Chlamydia trachomatis en un \u00e1rea del norte de Espa\u00f1a [Genotyping of Chlamydia trachomatis in an area of northern Spain]","volume":"27","author":"Montes","year":"2009","journal-title":"Enferm. Infecc. Microbiol. Clin."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1128\/JCM.42.4.1641-1647.2004","article-title":"Characterization of ompA genotypes by sequence analysis of DNA from all detected cases of Chlamydia trachomatis infections during 1 year of contact tracing in a Swedish County","volume":"42","author":"Osterlund","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1128\/JB.00895-09","article-title":"Evolutionary dynamics of ompA, the gene encoding the Chlamydia trachomatis key antigen","volume":"191","author":"Nunes","year":"2009","journal-title":"J. Bacteriol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2231","DOI":"10.1128\/JCM.00586-10","article-title":"Chlamydia trachomatis serovar distribution and Neisseria gonorrhoeae coinfection in male patients with urethritis in Greece","volume":"48","author":"Papadogeorgakis","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1099\/jmm.0.028076-0","article-title":"Genital chlamydial infection: Association between clinical features, organism genotype and load","volume":"60","author":"Jalal","year":"2011","journal-title":"J. Med. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"481890","DOI":"10.1155\/2011\/481890","article-title":"Chlamydia trachomatis genotypes and the Swedish new variant among urogenital Chlamydia trachomatis strains in Finland","volume":"2011","author":"Niemi","year":"2011","journal-title":"Infect. Dis. Obstet. Gynecol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1111\/j.1574-695X.2011.00843.x","article-title":"Genotyping of Chlamydia trachomatis directly from urogenital and conjunctiva samples using an ompA gene pyrosequencing-based assay","volume":"63","author":"Kese","year":"2011","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1007\/s00284-012-0106-7","article-title":"Distribution of Chlamydia trachomatis serotypes in clinical urogenital samples from north-eastern Croatia","volume":"64","author":"Lauc","year":"2012","journal-title":"Curr. Microbiol."},{"key":"ref_22","first-page":"215","article-title":"Chlamydia trachomatis serovar distribution and other sexually transmitted coinfections in subjects attending an STD outpatients clinic in Italy","volume":"35","author":"Marangoni","year":"2012","journal-title":"New Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1007\/s15010-012-0301-2","article-title":"Chlamydia trachomatis prevalence, genotype distribution and identification of the new Swedish variant in Southern Germany","volume":"41","author":"Fieser","year":"2013","journal-title":"Infection"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1136\/sextrans-2011-050062","article-title":"Chlamydia trachomatis serovars in community-based HIV-positive and HIV-negative men who have sex with men in Sydney, Australia","volume":"87","author":"Templeton","year":"2011","journal-title":"Sex. Transm. Infect."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"143","DOI":"10.7883\/yoken.64.143","article-title":"Prevalence of anorectal Chlamydia trachomatis infection and its genotype distribution among men who have sex with men in Shenzhen, China","volume":"64","author":"Li","year":"2011","journal-title":"Jpn. J. Infect. Dis."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1097\/OLQ.0b013e3181fc6944","article-title":"Chlamydia trachomatis genotypes among men who have sex with men in Australia","volume":"38","author":"Twin","year":"2011","journal-title":"Sex. Transm. Dis."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"4066","DOI":"10.1128\/JCM.00574-06","article-title":"Lymphogranuloma venereum prevalence in Sweden among men who have sex with men and characterization of Chlamydia trachomatis ompA genotypes","volume":"44","author":"Klint","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3548","DOI":"10.1128\/JCM.01713-12","article-title":"Chlamydia trachomatis strains show specific clustering for men who have sex with men compared to heterosexual populations in Sweden, the Netherlands, and the United States","volume":"50","author":"Christerson","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Quint, K.D., Bom, R.J., Quint, W.G., Bruisten, S.M., van der Loeff, M.F., Morr\u00e9, S.A., and de Vries, H.J. (2011). Anal infections with concomitant Chlamydia trachomatis genotypes among men who have sex with men in Amsterdam, the Netherlands. BMC Infect. Dis., 11.","DOI":"10.1186\/1471-2334-11-63"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1136\/sextrans-2011-050458","article-title":"Genotyping of Chlamydia trachomatis in rectal and pharyngeal specimens: Identification of LGV genotypes in Finland","volume":"88","author":"Korhonen","year":"2012","journal-title":"Sex. Transm. Infect."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1128\/IAI.01324-09","article-title":"Genome sequencing of recent clinical Chlamydia trachomatis strains identifies loci associated with tissue tropism and regions of apparent recombination","volume":"78","author":"Jeffrey","year":"2010","journal-title":"Infect. Immun."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1099\/jmm.0.026476-0","article-title":"Distribution of Chlamydia trachomatis genovars among youths and adults in Brazil","volume":"60","author":"Machado","year":"2011","journal-title":"J. Med. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"374","DOI":"10.7883\/yoken.JJID.2007.374","article-title":"Longitudinal epidemiology of Chlamydia trachomatis serovars in female patients in Japan","volume":"60","author":"Takahashi","year":"2007","journal-title":"Jpn. J. Infec.t Dis."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"7063e72","DOI":"10.1128\/IAI.72.12.7063-7072.2004","article-title":"Polymorphisms in the Chlamydia trachomatis cytotoxin locus associated with ocular and genital isolates","volume":"72","author":"Carlson","year":"2004","journal-title":"Infect. Immun."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"6407e18","DOI":"10.1128\/IAI.73.10.6407-6418.2005","article-title":"Comparative genomic analysis of Chlamydia trachomatis oculotropic and genitotropic strains","volume":"73","author":"Carlson","year":"2005","journal-title":"Infect. Immun."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1128\/JCM.00249-15","article-title":"Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries","volume":"53","author":"Herrmann","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Versteeg, B., van Rooijen, M.S., Schim van der Loeff, M.F., De Vries, H.J., and Bruisten, S.M. (2014). No indication for tissue tropism in urogenital and anorectal Chlamydia trachomatis infections using high-resolution multilocus sequence typing. BMC Infect. Dis., 14.","DOI":"10.1186\/1471-2334-14-464"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Rodr\u00edguez-Dom\u00ednguez, M., Gonz\u00e1lez-Alba, J.M., Puerta, T., Men\u00e9ndez, B., S\u00e1nchez-D\u00edaz, A.M., Cant\u00f3n, R., del Romero, J., and Gal\u00e1n, J.C. (2015). High Prevalence of Co-Infections by Invasive and Non-Invasive Chlamydia trachomatis Genotypes during the Lymphogranuloma Venereum Outbreak in Spain. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0126145"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1016\/j.cmi.2017.03.009","article-title":"Spread of a new Chlamydia trachomatis variant from men who have sex with men to the heterosexual population after replacement and recombination in ompA and pmpH genes","volume":"23","author":"Puerta","year":"2017","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.3201\/eid1108.050535","article-title":"Real-time polymerase chain reaction to diagnose lymphogranuloma venereum","volume":"11","author":"Spaargaren","year":"2005","journal-title":"Emerg. Infect. Dis."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1469-0691.2007.01786.x","article-title":"European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group on Epidemiological Markers (ESGEM). Guidelines for the validation and application of typing methods for use in bacterial epidemiology","volume":"13","author":"Tassios","year":"2007","journal-title":"Clin. Microbiol. Infect."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/8\/6941\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:12:33Z","timestamp":1760123553000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/8\/6941"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,8]]},"references-count":41,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2023,4]]}},"alternative-id":["ijms24086941"],"URL":"https:\/\/doi.org\/10.3390\/ijms24086941","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,8]]}}}