Natural Course of Chlamydia trachomatis Bacterial Load in the Time Interval between Screening and Treatment in Anogenital Samples

Comparison of analytical sensitivity of DNA-based and RNA-based nucleic acid amplification tests for reproductive tract infection pathogens: implications for clinical applications

Currently, DNA-based nucleic acid amplification tests (NAATs) and RNA-based NAATs are employed to detect reproductive tract infection (RTI) pathogens including Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Ureaplasma urealyticum (UU). Although evaluations of DNA-based NAATs have already existed, the comparison of the two methods is scarce. Thus, we compared the limits of detection (LODs) of DNA-based and RNA-based NAATs on the same experimental conditions. Inactivated culture supernatants of CT, NG, and UU with determined pathogen DNA and RNA load were used to evaluate LODs of seven DNA kits and one RNA kit. The LODs of the seven DNA kits for CT, NG, and UU ranged between 38-1,480, 94-20,011, and 132-2,011 copies/mL, respectively. As for RNA kits, they could detect samples at RNA concentrations of 3,116, 2,509, and 2,896 copies/mL, respectively. The RNA concentrations of CT, NG, and UU were 40, 885, and 42 times that of corresponding pathogen DNA concentrations in the employed supernatants, so RNA kits could detect pathogen DNA concentrations as low as 78 copies/mL, 3 copies/mL, and 69 copies/mL, respectively, but the level of pathogen load that the RNA tests could detect was primarily dependent on the infectious phase and transcriptional level of RNA. Thus, a schematic of bacterial dynamics during the period of reproductive tract infections was provided, which suggests that in terms of the analytical sensitivity of pathogen detection, RNA tests are more suitable for detecting active infection and recovery phase, while DNA tests are more suitable for detection in the early stage of infection. IMPORTANCE Reproductive tract infections have considerable effects on the health of humans. CT, NG , and UU are common pathogens. Although evaluation of DNA-based tests has already existed, the comparison between DNA-based and RNA-based tests is rare. Therefore, this study compared the limits of detection of the two tests on the same experimental conditions. Results suggested that most DNA-based NAATs could detect CT, NG, and UU at DNA concentrations lower than 1,000 copies/mL, while RNA-based NAATs could detect bacteria at RNA concentrations around 3,000 copies/mL. Considering the copy number of RNA per bacterium is dynamic through the growth cycle, further comparison is combined with a schematic of bacterial dynamics. Results suggested that in terms of the analytical sensitivity of pathogen detection, RNA tests are more suitable for detecting active infection and recovery phase, while DNA tests are more suitable for detection in the early stage of infection.

Men and Women Repeatedly Infected With Chlamydia trachomatis Have a Lower Urogenital Bacterial Load

We assessed whether patients repeatedly infected with Chlamydia trachomatis (CT) have a lower urogenital or anorectal CT load. A CT-positive retest was independently associated with higher vaginal and higher urine Cq values (P<0.01). Partial immunity could play a role in repeat urogenital infections, potentially not in anorectal infections.

Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades

The development of Subzymes demonstrates how the catalytic activity of DNAzymes can be controlled for detecting nucleic acids; however, Subzymes alone lack the sensitivity required to detect low target concentrations. To improve sensitivity, we developed a feedback system using a pair of cross-catalytic Subzymes. These were individually tethered to microparticles (MP) and separated by a porous membrane rendering them unable to interact. In the presence of a target, active PlexZymes^® cleave a first Subzyme, which separates a first DNAzyme from its MP, allowing the DNAzyme to migrate through the membrane, where it can cleave a second Subzyme. This releases a second DNAzyme which can now migrate through the membrane and cleave more of the first Subzyme, thus initiating a cross-catalytic cascade. Activated DNAzymes can additionally cleave fluorescent substrates, generating a signal, and thereby, indicating the presence of the target. The method detected 1 fM of DNA homologous to the ompA gene of Chlamydia trachomatis within 30 min, demonstrating a 10,000-fold increase in sensitivity over PlexZyme detection alone. The Subzyme cascade is universal and can be triggered by any target by modifying the target sensing arms of the PlexZymes. Further, it is isothermal, protein-enzyme-free and shows great potential for rapid and affordable biomarker detection.

Men and Women Have an Equal Oropharyngeal and Anorectal Chlamydia trachomatis Bacterial Load: A Comparison of 3 Anatomic Sites

BACKGROUND

The Chlamydia trachomatis bacterial load could have impact on transmission and sequelae. This is the first study providing comparison of C. trachomatis load at 3 anatomic sites estimated by cycle quantification (Cq) values.

METHODS

Data from 7900 C. trachomatis-positive samples were included (2012-2018). Cq value was used as an inversely proportional measure for C. trachomatis load. Multivariable linear regression analyses assessed differences in mean Cq values.

RESULTS

Vaginal swabs had the lowest Cq values (31.0) followed by urine (32.5), anorectal swabs (34.0), and oropharyngeal swabs (36.8) (P < .001). Men and women had similar oropharyngeal (36.4 vs 37.3; P = .13) and anorectal (34.2 vs 33.9; P = .19) Cq values. Men (32.2) and women (30.7) aged <25 years had lower urogenital Cq values than men (32.8) and women (31.9) aged ≥25 years (P < .001). HIV-positive patients had higher urogenital Cq values than HIV-negative patients (33.8 vs 32.6; P < .03).

CONCLUSIONS

Men and women have a similar C. trachomatis load at extragenital locations arguing for similar transmission potential and clinical relevance. Older patients and HIV-coinfected patients had lower C. trachomatis load, suggesting exposure to previous C. trachomatis infections potentially leading to partial immunity reducing load.

Chlamydia trachomatis bacterial load, estimated by Cq values, in urogenital samples from men and women visiting the general practice, hospital or STI clinic

Background

The bacterial load of Chlamydia trachomatis (CT) is assumed to play a role in transmission and sequelae. We assessed urogenital CT cycle quantification (Cq) values, as an indicator for CT load, of men and women diagnosed by general practitioners (GPs), hospital physicians and the STI clinic.

Methods

Urogenital CT-positive samples (n = 2,055 vaginal swabs, n = 77 cervical swabs, n = 1,519 urine samples and n = 19 urethral swabs) diagnosed by GPs, hospital physicians and the STI clinic from the Maastricht Medical Microbiology Laboratory were included (2012–2016). The outcome measure ‘urogenital Cq values’ was used as an inversely proportional measure for CT load. Among all patients, multivariate linear regression analyses were used to assess primary determinants for mean urogenital Cq values, stratified by sex. Additional clinical determinants were assessed among STI clinic patients.

Results

In men, mean urogenital Cq values were similar between GPs, hospital physicians and the STI clinic (32.7 and 33.5 vs. 32.7; p>0.05). Women visiting the GP had lower urogenital Cq values than women visiting the STI clinic (30.2 vs. 30.9; p = <0.001). Women visiting the hospital had higher urogenital Cq values than women visiting the STI clinic (32.4 vs. 30.9; p = <0.001). Among STI clinic women, urogenital Cq values were lower in women with concurrent anorectal CT and in rectally untested women compared to anorectal CT-negative women (30.7 and 30.6 vs. 33.9; p = <0.001).

Conclusion

Men visiting different STI care providers had similar urogenital Cq values, which could be an indicator for similar CT loads. The lower Cq values of women visiting the GP compared to women visiting the STI clinic could be an indicator for higher CT loads and likely higher transmission potential. Notably, urogenital Cq values of STI clinic women were much lower (>3 Cq) when STI clinic women also had anorectal CT. This finding could indicate higher urogenital CT loads and likely higher chances of transmission and sequelae.

Spontaneous clearance of urogenital, anorectal and oropharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae in women, MSM and heterosexual men visiting the STI clinic: a prospective cohort study

OBJECTIVE

Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections can clear without treatment. Despite high prevalence of anorectal infections in men who have sex with men (MSM) and women, studies on anorectal clearance are scarce. Moreover it is unknown whether bacterial load affects urogenital/anorectal CT clearance. In this prospective cohort study, CT and NG clearance is assessed at three anatomical sites of men and women.

METHODS

CT-positive and NG-positive MSM, heterosexual men and women ≥18 years of age visiting our STI clinic between 2011 and 2013 underwent a repeat test when returning for treatment (n=482). The primary outcome was clearance, defined as a positive nucleic acid amplification test (NAAT) at screening-consultation, followed by a negative NAAT at treatment-consultation. Sociodemographics, sexual risk behaviour and CT bacterial load (inhouse quantitative PCR) were tested as determinants for clearance using multivariable logistic regression for CT and Fisher's exact test for NG.

RESULTS

CT clearance was 9.1% (10/110) for urine, 6.8% (20/292) for vaginal swabs, 12.7% (8/63) for anorectal swabs (ie, 4.0% [1/25] in MSM and 18.4% [7/38] in women) and 57.1% (4/7) for oropharyngeal swabs. For NG this was 33.3% (2/6), 28.6% (2/7), 20.0% (2/10) and 27.3% (6/22), respectively. The number of days between tests (median 10, IQR 7-14) was not associated with clearance. Lower bacterial load at screening was the only predictor for CT clearance (urine mean 1.2 vs 2.6 log CT/mL, p=0.001; vaginal swabs mean 2.1 vs 5.2 log CT/mL p<0.0001; anorectal swabs mean 2.0 vs 3.7 log CT/mL, p=0.002). None of the tested determinants were associated with NG clearance.

CONCLUSIONS

This study reports the largest number of anorectal infections tested for CT and NG clearance to date. Clearance in all sample types was substantial: between 7% and 57% for CT, and between 20% and 33% for NG (notwithstanding low absolute numbers). CT clearance was associated with a lower load at screening. However, not all individuals with low bacterial CT load cleared the infection, hampering STI guideline change.

Review of Chlamydia trachomatis viability methods: assessing the clinical diagnostic impact of NAAT positive results

INTRODUCTION

Chlamydia trachomatis (chlamydia) is the most commonly diagnosed bacterial sexually transmitted infection (STI) worldwide. The advancement of molecular techniques has made chlamydia diagnostics infinitely easier. However, molecular techniques lack the information on chlamydia viability. Where in routine diagnostics the detection of chlamydia DNA or RNA might suffice, in other patient scenarios, information on the viability of chlamydia might be essential. Areas covered: In this review, the authors discuss the specific strengths and limitations of currently available methods to evaluate chlamydia viability: conventional cell culture, messenger RNA (mRNA) detection and viability-PCR (V-PCR). PubMed and Google Scholar were searched with the following terms: Chlamydia trachomatis, Treatment failure, Anal chlamydia, Microbial viability, Culture, Viability-PCR, Messenger RNA, and Molecular diagnostics Expert commentary: Several techniques are currently available to determine chlamydia viability and thus the clinical relevance of a positive test result in clinical samples. Depending on the underlying research question, all three discussed techniques have their merits when testing for viability. However, mRNA methods show the most promise in determining the presence of a true infection, in case the chlamydia reticulate body can be specifically detected. Further research is needed to understand how to best apply viability testing in current chlamydia diagnostics.

Viability-PCR Shows That NAAT Detects a High Proportion of DNA from Non-Viable Chlamydia trachomatis

Objectives

According to the current guidelines for laboratory diagnosis of sexually transmitted infections (STIs), nucleic acid amplification tests (NAATs) are the preferred diagnostic method for Chlamydia trachomatis (CT) infections. However, NAATs amplify the available target DNA without discriminating between DNA originating from viable or non-viable CT. Assessing CT viability will provide more insights in the clinical and public health relevance of a CT positive test result. The aim of this study was to technically validate and implement viability-PCR (V-PCR) to asses CT viability.

Methods

Technical validation of V-PCR was performed by the assessment of predefined viability ratios of CT. Samples were subjected to V-PCR which consisted of propidium monoazide (PMA) treatment prior to DNA extraction followed by quantitative PCR (qPCR) targeting the ompA gene for the detection of CT DNA. Finally, V-PCR was applied to vaginal swabs of 50 CT positive patients, as indicated by routine NAAT, collected at our outpatient STD clinics before antimicrobial treatment.

Results

Technical validation of V-PCR showed that PMA treatment of heat-inactivated CT culture resulted in an almost complete loss of qPCR signal. PMA treated samples of the fresh viable CT culture showed no marked reduction of PCR signal, indicating that all DNA from viable CT could be detected. Applying V-PCR to clinical samples showed that in 36% of samples (18/50) less than 1% of CT DNA originated from viable bacteria.

Conclusions

V-PCR showed to be a fast and easy method to assess CT viability in clinical samples, without the need of traditional challenging cell culture methods. Furthermore, V-PCR results of clinical samples have indicated that a substantial amount of the amplified CT DNA originated from non-viable cells. Although results might be influenced by cell death during transport, this study suggests that there is a potential overestimation of quantitative CT positivity by currently used NAATs.