Diagnostic-avoiding Chlamydia Trachomatis Variants Detected in Cervical and Endometrial Specimens from Women During 16S Microbiome Profiling

Overview

Journal BMC Infect Dis

Publisher Biomed Central

Specialty Infectious Diseases

Date 2025 Mar 13

PMID 40075274

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 OConnell

Affiliations

Soon will be listed here.

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 Combo 2 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, G1523A nucleotide polymorphism 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 was circulating in the northeastern US prior to its detection and characterization in 2019. Although infrequent, false negative tests could represent infection with probe-avoidant CT mutants. Additional research is needed to determine if there is a role for CT tests using alternate probes for symptomatic or exposed individuals suspected of infection with these mutant chlamydial strains.

References

Unemo M, Hansen M, Hadad R, Puolakkainen M, Westh H, Rantakokko-Jalava K . Sensitivity, specificity, inclusivity and exclusivity of the updated Aptima Combo 2 assay, which provides detection coverage of the new diagnostic-escape Chlamydia trachomatis variants. BMC Infect Dis. 2020; 20(1):419. PMC: 7298785. DOI: 10.1186/s12879-020-05148-7. View

Mitchev N, Singh R, Ramsuran V, Ismail A, Allam M, Kwenda S . Assessment of Antibiotic Resistance and Efflux Pump Gene Expression in Neisseria Gonorrhoeae Isolates from South Africa by Quantitative Real-Time PCR and Regression Analysis. Int J Microbiol. 2022; 2022:7318325. PMC: 9616671. DOI: 10.1155/2022/7318325. View

Tabrizi S, Unemo M, Limnios A, Hogan T, Hjelmevoll S, Garland S . Evaluation of six commercial nucleic acid amplification tests for detection of Neisseria gonorrhoeae and other Neisseria species. J Clin Microbiol. 2011; 49(10):3610-5. PMC: 3187337. DOI: 10.1128/JCM.01217-11. View

Rantakokko-Jalava K, Hokynar K, Hieta N, Keskitalo A, Jokela P, Muotiala A . samples testing falsely negative in the Aptima Combo 2 test in Finland, 2019. Euro Surveill. 2019; 24(22). PMC: 6549458. DOI: 10.2807/1560-7917.ES.2019.24.22.1900298. View

Matysiak C, Cheng A, Kirby J . Evaluation of the Abbott Alinity m STI assay for diagnosis of the primary causes of sexually transmitted infections in the United States. Pract Lab Med. 2023; 36:e00332. PMC: 10495529. DOI: 10.1016/j.plabm.2023.e00332. View

Roberts D, Davis G, Cole M, Naik D, Maru H, Woodford N . Prevalence of new variants of escaping detection by the Aptima Combo 2 assay, England, June to August 2019. Euro Surveill. 2019; 24(38). PMC: 6761577. DOI: 10.2807/1560-7917.ES.2019.24.38.1900557. View

. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae--2014. MMWR Recomm Rep. 2014; 63(RR-02):1-19. PMC: 4047970. View

Karellis A, Naeem F, Nair S, Mallya S, Routy J, Gahagan J . Multiplexed rapid technologies for sexually transmitted infections: a systematic review. Lancet Microbe. 2022; 3(4):e303-e315. DOI: 10.1016/S2666-5247(21)00191-9. View

Cole J, Wang Q, Fish J, Chai B, McGarrell D, Sun Y . Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2013; 42(Database issue):D633-42. PMC: 3965039. DOI: 10.1093/nar/gkt1244. View

10.

Liu C, Hufnagel K, OConnell C, Goonetilleke N, Mokashi N, Waterboer T . Reduced Endometrial Ascension and Enhanced Reinfection Associated With Immunoglobulin G Antibodies to Specific Chlamydia trachomatis Proteins in Women at Risk for Chlamydia. J Infect Dis. 2021; 225(5):846-855. PMC: 8889297. DOI: 10.1093/infdis/jiab496. View

11.

Ripa T, Nilsson P . A variant of Chlamydia trachomatis with deletion in cryptic plasmid: implications for use of PCR diagnostic tests. Euro Surveill. 2007; 11(11):E061109.2. DOI: 10.2807/esw.11.45.03076-en. View

12.

Katz S, Danavall D, Morris M, Herrod B, Dale S, Nye M . Chlamydia trachomatis Variants Escaping Detection in the Aptima Combo 2 Assay in the United States. Sex Transm Dis. 2022; 49(6):448-452. PMC: 9133125. DOI: 10.1097/OLQ.0000000000001617. View

13.

Bristow C, McGrath M, Cohen A, Anderson L, Gordon K, Klausner J . Comparative Evaluation of 2 Nucleic Acid Amplification Tests for the Detection of Chlamydia trachomatis and Neisseria gonorrhoeae at Extragenital Sites. Sex Transm Dis. 2017; 44(7):398-400. PMC: 5486408. DOI: 10.1097/OLQ.0000000000000627. View

14.

Zheng X, OConnell C, Zhong W, Nagarajan U, Tripathy M, Lee D . Discovery of Blood Transcriptional Endotypes in Women with Pelvic Inflammatory Disease. J Immunol. 2018; 200(8):2941-2956. PMC: 5893373. DOI: 10.4049/jimmunol.1701658. View

15.

Golparian D, Tabrizi S, Unemo M . Analytical specificity and sensitivity of the APTIMA Combo 2 and APTIMA GC assays for detection of commensal Neisseria species and Neisseria gonorrhoeae on the Gen-Probe Panther instrument. Sex Transm Dis. 2013; 40(2):175-8. DOI: 10.1097/OLQ.0b013e3182787e45. View

16.

Taylor B, Zheng X, OConnell C, Wiesenfeld H, Hillier S, Darville T . Risk factors for endometritis and incident infection: a secondary data analysis of the T cell Response Against Chlamydia (TRAC) Study. Sex Transm Infect. 2018; 94(6):414-420. PMC: 6295147. DOI: 10.1136/sextrans-2017-053376. View

17.

Russell A, Zheng X, OConnell C, Taylor B, Wiesenfeld H, Hillier S . Analysis of Factors Driving Incident and Ascending Infection and the Role of Serum Antibody in Chlamydia trachomatis Genital Tract Infection. J Infect Dis. 2015; 213(4):523-31. PMC: 4721908. DOI: 10.1093/infdis/jiv438. View

18.

Darville T, Albritton H, Zhong W, Dong L, OConnell C, Poston T . Anti-chlamydia IgG and IgA are insufficient to prevent endometrial chlamydia infection in women, and increased anti-chlamydia IgG is associated with enhanced risk for incident infection. Am J Reprod Immunol. 2019; 81(5):e13103. PMC: 6475609. DOI: 10.1111/aji.13103. View

19.

Edgar R . Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26(19):2460-1. DOI: 10.1093/bioinformatics/btq461. View

20.

Liu C, Mokashi N, Darville T, Sun X, OConnell C, Hufnagel K . 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. Microbiol Spectr. 2023; 11(4):e0468922. PMC: 10434056. DOI: 10.1128/spectrum.04689-22. View