{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T13:29:16Z","timestamp":1768570156927,"version":"3.49.0"},"posted":{"date-parts":[[2024,11,13]]},"group-title":"Infectious Diseases (except HIV\/AIDS)","reference-count":48,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,11,13]],"date-time":"2024-11-13T00:00:00Z","timestamp":1731456000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.medrxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,12,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>\n                    Performance of a 16S rRNA analysis of the cervicovaginal microbiome of 220 participants recruited into the T Cell Response against Chlamydia (TRAC) cohort between February 2011 and August 2014 in Allegheny County, Pennsylvania USA detected DNA encoding chlamydial 16S rRNA in samples from seven participants whose tests were negative for\n                    <jats:italic>Chlamydia trachomatis<\/jats:italic>\n                    (CT) and DNA encoding gonococcal 16S rRNA from five participants whose tests were negative for\n                    <jats:italic>Neisseria gonorrhoeae<\/jats:italic>\n                    (NG) infection with the Aptima Combo2 assay (Hologic).\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We used targeted PCR amplification followed by sequencing to characterize the chlamydial 23S rRNA locus and qPCR to detect gonococcal DNA in residual diagnostic swab eluates or DNA used to generate 16S rRNA libraries.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Discrepant specimens that contained chlamydial DNA carried a diagnostic-avoidant, G1526A variant in the 23S rRNA locus identical to variants previously detected in Finland, Denmark, and the UK. PCR validation of gonococcal DNA was confirmed for all participants whose tests were negative, with stochastic effects consistent with infection levels close to the limit of detection by the diagnostic assay.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>These data indicate that this probe-avoidant CT mutant, and possibly others, were circulating in the northeastern US prior to their detection and characterization in 2019. Although infrequent, documentation of false negative results for CT indicates a need for clinicians to consider performance of a second test that uses alternate PCR targets if patients have persistent symptoms or have known contact to an infected sex partner and their initial NAAT is negative.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2024.11.13.24316066","type":"posted-content","created":{"date-parts":[[2024,11,13]],"date-time":"2024-11-13T17:45:16Z","timestamp":1731519916000},"source":"Crossref","is-referenced-by-count":1,"title":["Diagnostic-avoiding\n                  <i>Chlamydia trachomatis<\/i>\n                  variants detected in cervical and endometrial specimens from women during 16S microbiome profiling"],"prefix":"10.64898","author":[{"given":"Sangmi","family":"Jeong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tammy","family":"Tollison","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hayden","family":"Brochu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hsuan","family":"Chou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tammy","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Priyanka","family":"Baghaie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7050-0164","authenticated-orcid":false,"given":"Kacy S.","family":"Yount","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1507-2202","authenticated-orcid":false,"given":"Toni","family":"Darville","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harold C","family":"Wiesenfeld","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sharon L","family":"Hillier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0117-3582","authenticated-orcid":false,"given":"Xinxia","family":"Peng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8229-684X","authenticated-orcid":false,"given":"Catherine M.","family":"O\u2019Connell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2024120912351104000_2024.11.13.24316066v2.1","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiv438"},{"key":"2024120912351104000_2024.11.13.24316066v2.2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiw485"},{"issue":"0","key":"2024120912351104000_2024.11.13.24316066v2.3","first-page":"e04689","article-title":"A Machine Learning-Based Analytic Pipeline Applied to Clinical and Serum IgG Immunoproteome Data To Predict Chlamydia trachomatis Genital Tract Ascension and Incident Infection in Women","volume":"0","year":"2023","journal-title":"Microbiology Spectrum"},{"key":"2024120912351104000_2024.11.13.24316066v2.4","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiab496"},{"key":"2024120912351104000_2024.11.13.24316066v2.5","doi-asserted-by":"publisher","DOI":"10.1111\/aji.13103"},{"key":"2024120912351104000_2024.11.13.24316066v2.6","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiz087"},{"key":"2024120912351104000_2024.11.13.24316066v2.7","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1701658"},{"issue":"Supplement_2","key":"2024120912351104000_2024.11.13.24316066v2.8","doi-asserted-by":"crossref","first-page":"S64","DOI":"10.1093\/infdis\/jiab149","article-title":"Host Genetic Risk Factors for Chlamydia trachomatis-Related Infertility in Women","volume":"224","year":"2021","journal-title":"J Infect Dis"},{"issue":"307","key":"2024120912351104000_2024.11.13.24316066v2.9","first-page":"307","article-title":"Gene Expression Signatures Can Aid Diagnosis of Sexually Transmitted Infection-Induced Endometritis in Women","volume":"8","year":"2018","journal-title":"Front Cell Infect Microbiol"},{"key":"2024120912351104000_2024.11.13.24316066v2.10","doi-asserted-by":"publisher","DOI":"10.1136\/sextrans-2017-053376"},{"key":"2024120912351104000_2024.11.13.24316066v2.11","doi-asserted-by":"crossref","unstructured":"Jeong S , Tollison T , Brochu H , Chou H , Huntress I , Yount KS , Zheng X , Darville T , O\u2019Connell CM , Peng X : Cervicovaginal microbial features predicts <em>Chlamydia trachomatis<\/em> spread to the upper genital tract of infected women. bioRxiv 2024:2024.2011.2026.625070.","DOI":"10.1101\/2024.11.26.625070"},{"key":"2024120912351104000_2024.11.13.24316066v2.12","doi-asserted-by":"publisher","DOI":"10.1136\/sextrans-2021-054988"},{"issue":"6","key":"2024120912351104000_2024.11.13.24316066v2.13","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1111\/apm.13043","article-title":"A Chlamydia trachomatis 23S rRNA G1523A variant escaping detection in the Aptima Combo 2 assay (Hologic) was widespread across Denmark in July-September 2019","volume":"128","year":"2020","journal-title":"APMIS"},{"key":"2024120912351104000_2024.11.13.24316066v2.14","doi-asserted-by":"crossref","unstructured":"Roberts DJ , Davis GS , Cole MJ , Naik D , Maru H , Woodford N , Muir P , Horner P , Simms I , Thickett G et al: Prevalence of new variants of Chlamydia trachomatis escaping detection by the Aptima Combo 2 assay, England, June to August 2019. Euro Surveill 2019, 24(38).","DOI":"10.2807\/1560-7917.ES.2019.24.38.1900557"},{"key":"2024120912351104000_2024.11.13.24316066v2.15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq461"},{"key":"2024120912351104000_2024.11.13.24316066v2.16","doi-asserted-by":"publisher","DOI":"10.15698\/mic2019.03.672"},{"key":"2024120912351104000_2024.11.13.24316066v2.17","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268813003488"},{"key":"2024120912351104000_2024.11.13.24316066v2.18","first-page":"7318325","article-title":"Assessment of Antibiotic Resistance and Efflux Pump Gene Expression in Neisseria Gonorrhoeae Isolates from South Africa by Quantitative Real-Time PCR and Regression Analysis","volume":"2022","year":"2022","journal-title":"Int J Microbiol"},{"issue":"8","key":"2024120912351104000_2024.11.13.24316066v2.19","doi-asserted-by":"crossref","first-page":"227","DOI":"10.3390\/microorganisms7080227","article-title":"The Finnish new variant of Chlamydia trachomatis with a single nucleotide polymorphism in the 23S rRNA target escapes detection by the Aptima Combo 2 test","volume":"7","year":"2019","journal-title":"Microorganisms"},{"key":"2024120912351104000_2024.11.13.24316066v2.20","unstructured":"R: A Language and Environment for Statistical Computing. In. Edited by Team RC: R Foundation for Statistical Computing; 2015."},{"key":"2024120912351104000_2024.11.13.24316066v2.21","unstructured":"Wickham H : ggplot: Elegant graphics for data analysis. New York: Springer-Verlag 2016."},{"key":"2024120912351104000_2024.11.13.24316066v2.22","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1244"},{"key":"2024120912351104000_2024.11.13.24316066v2.23","unstructured":"Robert CE : SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences. bioRxiv 2016:074161."},{"key":"2024120912351104000_2024.11.13.24316066v2.24","doi-asserted-by":"publisher","DOI":"10.7326\/0003-4819-142-11-200506070-00010"},{"issue":"RR-02","key":"2024120912351104000_2024.11.13.24316066v2.25","first-page":"1","article-title":"Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae--2014","volume":"63","author":"Centers for Disease C, Prevention","year":"2014","journal-title":"MMWR Recomm Rep"},{"issue":"1","key":"2024120912351104000_2024.11.13.24316066v2.26","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1186\/s12879-020-05148-7","article-title":"Sensitivity, specificity, inclusivity and exclusivity of the updated Aptima Combo 2 assay, which provides detection coverage of the new diagnostic-escape Chlamydia trachomatis variants","volume":"20","year":"2020","journal-title":"BMC Infect Dis"},{"key":"2024120912351104000_2024.11.13.24316066v2.27","doi-asserted-by":"crossref","unstructured":"Rantakokko-Jalava K , Hokynar K , Hieta N , Keskitalo A , Jokela P , Muotiala A , Jokiranta TS , Kuusela R , Sarkkinen H , Aittoniemi J et al: Chlamydia trachomatis samples testing falsely negative in the Aptima Combo 2 test in Finland, 2019. Euro Surveill 2019, 24(22).","DOI":"10.2807\/1560-7917.ES.2019.24.22.1900298"},{"key":"2024120912351104000_2024.11.13.24316066v2.28","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026162"},{"key":"2024120912351104000_2024.11.13.24316066v2.29","doi-asserted-by":"crossref","unstructured":"Abrams AJ , Trees DL , Nicholas RA : Complete Genome Sequences of Three Neisseria gonorrhoeae Laboratory Reference Strains, Determined Using PacBio Single-Molecule Real-Time Technology. Genome Announc 2015, 3(5).","DOI":"10.1128\/genomeA.01052-15"},{"key":"2024120912351104000_2024.11.13.24316066v2.30","doi-asserted-by":"publisher","DOI":"10.1136\/sextrans-2021-055360"},{"issue":"6","key":"2024120912351104000_2024.11.13.24316066v2.31","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1097\/OLQ.0000000000001617","article-title":"Chlamydia trachomatis Variants Escaping Detection in the Aptima Combo 2 Assay in the United States","volume":"49","year":"2022","journal-title":"Sex Transm Dis"},{"issue":"5","key":"2024120912351104000_2024.11.13.24316066v2.32","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1016\/j.cmi.2023.02.009","article-title":"The diagnostic-escape Finnish new variant of Chlamydia trachomatis first described in 2019 remains present in Finland three years after the introduction of an updated Aptima Combo 2 assay","volume":"29","year":"2023","journal-title":"Clin Microbiol Infect"},{"issue":"7","key":"2024120912351104000_2024.11.13.24316066v2.33","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1097\/OLQ.0000000000000627","article-title":"Comparative evaluation of two nucleic acid amplification tests for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae at extragenital sites","volume":"44","year":"2017","journal-title":"Sexually transmitted diseases"},{"key":"2024120912351104000_2024.11.13.24316066v2.34","doi-asserted-by":"publisher","DOI":"10.1097\/OLQ.0b013e3182787e45"},{"key":"2024120912351104000_2024.11.13.24316066v2.35","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01217-11"},{"key":"2024120912351104000_2024.11.13.24316066v2.36","doi-asserted-by":"crossref","first-page":"e00332","DOI":"10.1016\/j.plabm.2023.e00332","article-title":"Evaluation of the Abbott Alinity m STI assay for diagnosis of the primary causes of sexually transmitted infections in the United States","volume":"36","year":"2023","journal-title":"Pract Lab Med"},{"key":"2024120912351104000_2024.11.13.24316066v2.37","doi-asserted-by":"publisher","DOI":"10.1177\/0956462415615775"},{"key":"2024120912351104000_2024.11.13.24316066v2.38","unstructured":"Administration USFD: Alinity m CMV Assay - P210022. In.; 2022."},{"key":"2024120912351104000_2024.11.13.24316066v2.39","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-004-1257-7"},{"key":"2024120912351104000_2024.11.13.24316066v2.40","doi-asserted-by":"publisher","DOI":"10.1097\/OLQ.0b013e3181ffa7dc"},{"key":"2024120912351104000_2024.11.13.24316066v2.41","doi-asserted-by":"publisher","DOI":"10.1046\/j.1442-2042.2003.00621.x"},{"key":"2024120912351104000_2024.11.13.24316066v2.42","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.mm6521a5"},{"key":"2024120912351104000_2024.11.13.24316066v2.43","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00309-13"},{"key":"2024120912351104000_2024.11.13.24316066v2.44","doi-asserted-by":"crossref","unstructured":"Sukhum KV , Jean S , Wallace M , Anderson N , Burnham CA , Dantas G : Genomic Characterization of Emerging Bacterial Uropathogen Neisseria meningitidis, Which Was Misidentified as Neisseria gonorrhoeae by Nucleic Acid Amplification Testing. J Clin Microbiol 2021, 59(2).","DOI":"10.1128\/JCM.01699-20"},{"key":"2024120912351104000_2024.11.13.24316066v2.45","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.1.181"},{"issue":"11","key":"2024120912351104000_2024.11.13.24316066v2.46","first-page":"E061109","article-title":"A variant of Chlamydia trachomatis with deletion in cryptic plasmid: implications for use of PCR diagnostic tests","volume":"11","year":"2006","journal-title":"EuroSurveill"},{"key":"2024120912351104000_2024.11.13.24316066v2.47","doi-asserted-by":"crossref","unstructured":"Unemo M , Seth-Smith HM , Cutcliffe LT , Skilton RJ , Barlow D , Goulding D , Persson K , Harris SR , Kelly A , Bjartling C et al: The Swedish new variant of Chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization. Microbiology, 156(Pt 5):1394\u20131404.","DOI":"10.1099\/mic.0.036830-0"},{"issue":"4","key":"2024120912351104000_2024.11.13.24316066v2.48","doi-asserted-by":"crossref","first-page":"e303","DOI":"10.1016\/S2666-5247(21)00191-9","article-title":"Multiplexed rapid technologies for sexually transmitted infections: a systematic review","volume":"3","year":"2022","journal-title":"Lancet Microbe"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2024.11.13.24316066","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T20:20:10Z","timestamp":1768508410000},"score":1,"resource":{"primary":{"URL":"http:\/\/medrxiv.org\/lookup\/doi\/10.1101\/2024.11.13.24316066"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,13]]},"references-count":48,"URL":"https:\/\/doi.org\/10.1101\/2024.11.13.24316066","relation":{},"subject":[],"published":{"date-parts":[[2024,11,13]]},"subtype":"preprint"}}