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This study investigated anatomical site-specific prevalence and genotypes of CT among MSM recruited from three geographic areas in China.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We collected urine specimens and anorectal, pharyngeal swab specimens from 379 MSM. CT infection was identified using polymerase chain reaction and CT genotyping was determined by sequences of the ompA gene.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The results indicated that the overall prevalence of CT infection was 18.2% (95% confidence intervals [CIs], 13.9\u201322.5%) and significantly different between the cities (<jats:italic>p<\/jats:italic>\u2009=\u20090.048). The infection was most common at the anorectal site (15.6, 95%CIs 11.6\u201319.5%) followed by urethral (3.2, 95%CIs 1.4\u20135.0%) and oropharyngeal sites (1.6, 95%CIs 0.3\u20132.9%). Genotypes D and G were the most common CT strains in this population but genotype D was significantly predominated in Nanjing while genotype G was in Wuhan. No genotype related to lymphogranuloma venereum was found. CT infection was significantly related to the infection of<jats:italic>Neisseria gonorrhoeae<\/jats:italic>(adjusted odds ratio [aOR] 14.27, 95%CIs 6.02\u201333.83,<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.001) and age. Men older than 40\u2009years old were less likely to have a CT infection as compared to men under 30\u2009years old (aOR 0.37, 95% CIs 0.15\u20130.93,<jats:italic>p<\/jats:italic>\u2009=\u20090.03).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The high CT infection prevalence, particularly in the anorectal site, among MSM suggests the necessity to development an integrated CT screening and treatment program specifically focusing on this high-risk population. Surveillance of CT infections should be improved by including both infection and genotype based surveys into the current surveillance programs in China.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12879-019-4664-1","type":"journal-article","created":{"date-parts":[[2019,12,10]],"date-time":"2019-12-10T11:04:07Z","timestamp":1575975847000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Anatomical site prevalence and genotypes of Chlamydia trachomatis infections among men who have sex with men: a multi-site study in China"],"prefix":"10.1186","volume":"19","author":[{"given":"Ying","family":"Zhou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Mao","family":"Cai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shi-Liang","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ning-Xiao","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao-Feng","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Han","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue-Ping","family":"Yin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3927-2065","authenticated-orcid":false,"given":"Xiang-Sheng","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,12,10]]},"reference":[{"issue":"12","key":"4664_CR1","doi-asserted-by":"publisher","first-page":"e0143304","DOI":"10.1371\/journal.pone.0143304","volume":"10","author":"L Newman","year":"2015","unstructured":"Newman L, Rowley J, Vander Hoorn S, Wijesooriya NS, Unemo M, Low N, et al. 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We informed all study participants of the study details prior to their recruitment. Each study participant gave his written consent prior to enrollment.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"This is not applicable because no details, pictures or videos of any individual are disclosed in the manuscript.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"None of the authors reported any conflicts of interest.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1041"}}