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Previous studies have reported that <jats:italic>Chlamydia trachomatis<\/jats:italic> infection alters the vaginal microbiota of infected women. This study investigated differences in the vaginal microbiome of South African pregnant women living with HIV with and without <jats:italic>C. trachomatis<\/jats:italic> infection.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>This was a cross-sectional study among 385 pregnant women, recruited from the King Edward VIII Hospital in Durban, South Africa. <jats:italic>C. trachomatis<\/jats:italic> was detected using the Applied Biosystems\u2122 TaqMan<jats:sup>\u00ae<\/jats:sup> Assays. A total of 40 samples, 20 <jats:italic>C. trachomatis<\/jats:italic> positive and 20 <jats:italic>C. trachomatis<\/jats:italic> negative, were selected for sequencing. The sequencing of the vaginal microbiome was performed using the PacBio platform. Statistical analysis was performed on IBM SPSS version 26.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The prevalence of <jats:italic>C. trachomatis<\/jats:italic> infection was 12.2% (47\/385). The genus <jats:italic>Gardnerella<\/jats:italic> (32.14% vs. 24.02%) and species in the genus <jats:italic>Gardnerella<\/jats:italic> (31.97% vs. 24.03%) were more abundant in the <jats:italic>C. trachomatis<\/jats:italic>-infected group compared to the uninfected group. <jats:italic>Lactobacillus iners<\/jats:italic> were also more abundant in the <jats:italic>C. trachomatis<\/jats:italic>-infected women (28.30%) compared to the uninfected women. However, these observed patterns did not reach statistical significance. Discriminant analysis showed that the class <jats:italic>Alpha-Proteobacteria<\/jats:italic>; order <jats:italic>Bacillales<\/jats:italic>; family <jats:italic>Enterococcaceae<\/jats:italic>; the genera <jats:italic>Enhydrobacter<\/jats:italic>, <jats:italic>Enterococcus<\/jats:italic>, and <jats:italic>Parabacteroides<\/jats:italic>; <jats:italic>Enterococcus<\/jats:italic> spp.; and <jats:italic>Pseudomonas stutzeri<\/jats:italic> significantly contributed to a model separating <jats:italic>C. trachomatis<\/jats:italic>-infected women from the uninfected group (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The organisms and taxa that significantly contributed to separating the vaginal microbiota of <jats:italic>C. trachomatis<\/jats:italic>-infected women from the uninfected women in this study cohort have not been previously observed in association with <jats:italic>C. trachomatis<\/jats:italic> infection or the vaginal microbiota. Future studies in larger cohorts that will investigate the role of these microorganisms in <jats:italic>C. trachomatis<\/jats:italic> infection and the vaginal microbiota are required.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12905-024-03246-1","type":"journal-article","created":{"date-parts":[[2024,7,18]],"date-time":"2024-07-18T10:02:03Z","timestamp":1721296923000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The vaginal microbiome of South African pregnant women living with human immunodeficiency virus (HIV) with and without Chlamydia trachomatis infection"],"prefix":"10.1186","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6313-2735","authenticated-orcid":false,"given":"Nonkululeko G.","family":"Mabaso","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1573-4520","authenticated-orcid":false,"given":"Bongekile","family":"Ngobese","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hamilton","family":"Ganesan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Donald","family":"van der Westhuizen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wail M.","family":"Hassan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2392-0574","authenticated-orcid":false,"given":"Nathlee S.","family":"Abbai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,7,18]]},"reference":[{"issue":"11","key":"3246_CR1","doi-asserted-by":"publisher","first-page":"e0224658","DOI":"10.1371\/journal.pone.0224658","volume":"14","author":"HC Cheong","year":"2019","unstructured":"Cheong HC, Yap PSX, Chong CW, Cheok YY, Lee CYQ, Tan GMY, et al. 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