Diagnostic-avoiding Chlamydia trachomatis variants detected in cervical and endometrial specimens from women during 16S microbiome profiling.

Sangmi Jeong, Tammy Tollison, Hayden Brochu, Hsuan Chou, Tammy Yu, Priyanka Baghaie, Kacy S Yount, Toni Darville, Harold C Wiesenfeld, Sharon L Hillier, Xinxia Peng, Catherine M O'Connell
{"title":"Diagnostic-avoiding Chlamydia trachomatis variants detected in cervical and endometrial specimens from women during 16S microbiome profiling.","authors":"Sangmi Jeong, Tammy Tollison, Hayden Brochu, Hsuan Chou, Tammy Yu, Priyanka Baghaie, Kacy S Yount, Toni Darville, Harold C Wiesenfeld, Sharon L Hillier, Xinxia Peng, Catherine M O'Connell","doi":"10.1101/2024.11.13.24316066","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>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 Chlamydia trachomatis (CT) and DNA encoding gonococcal 16S rRNA from five participants whose tests were negative for Neisseria gonorrhoeae (NG) infection with the Aptima Combo2 assay (Hologic).</p><p><strong>Methods: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":94281,"journal":{"name":"medRxiv : the preprint server for health sciences","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11601777/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"medRxiv : the preprint server for health sciences","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2024.11.13.24316066","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

Abstract

Background: 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 Chlamydia trachomatis (CT) and DNA encoding gonococcal 16S rRNA from five participants whose tests were negative for Neisseria gonorrhoeae (NG) infection with the Aptima Combo2 assay (Hologic).

Methods: 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.

Results: 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.

Conclusions: 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.

在 16S 微生物组图谱分析过程中,从一组性活跃的顺性女性宫颈和子宫内膜标本中检测到的 Aptima Combo2-avoiding 变异。
背景:对2011年2月至2014年8月期间在美国宾夕法尼亚州阿勒格尼县招募的T细胞抗衣原体(TRAC)队列的220名参与者的宫颈阴道微生物组进行了16S rRNA分析、用 Aptima Combo2 检测法(Hologic)在 7 名沙眼衣原体 (CT) 检测呈阴性的参与者样本中检测到了编码衣原体 16S rRNA 的 DNA,在 5 名淋病奈瑟菌 (NG) 感染检测呈阴性的参与者样本中检测到了编码淋球菌 16S rRNA 的 DNA。方法:我们使用靶向 PCR 扩增和测序来确定衣原体 23S rRNA 位点的特征,并使用 qPCR 检测残留诊断拭子洗脱液或用于生成 16S rRNA 文库的 DNA 中的淋球菌 DNA:结果:含有衣原体 DNA 的不确定标本携带了一种诊断规避型 23S rRNA 基因座 G1526A 变体,该变体与之前在芬兰、丹麦和英国检测到的变体相同。所有检测结果呈阴性的参与者都证实了淋球菌 DNA 的 PCR 验证,随机效应与感染水平接近诊断测定的检测极限相一致:这些数据表明,在 2019 年及其后检测到并确定其特征之前,这种探针规避 CT 突变体以及其他可能的突变体已在美国东北部地区流行。尽管 CT 的假阴性结果并不常见,但其记录表明,如果患者症状持续存在或已知与受感染的性伴侣有接触,而其初次 NAAT 结果为阴性,则临床医生有必要考虑进行第二次检测,即使用替代 PCR 探针进行检测。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信