Evaluation of the cobas 4800 CT/NG Test for detecting Chlamydia trachomatis and Neisseria gonorrhoeae DNA in urogenital swabs and urine specimens

The association between adverse pregnancy outcomes with genital Chlamydia Trachomatis infection among pre-pregnancy couples in Shenzhen, China: A cross-sectional study

Objectives

To investigate the prevalence of adverse pregnancy outcomes (APOs) in women and the impact of pre-pregnancy couples' genital Chlamydia Trachomatis (GCT) infection and other infections on APOs.

Study design

Data on genital infections were collected from the Free Pre-pregnancy Health Check (FPHC) in Shenzhen, China. Data on APOs were collected from a 1-year telephone follow-up of pregnancy status and subsequent pregnancy outcomes.

Methods

APO data were used to count adverse outcomes, and logistic regression was conducted to determine the association between APOs and GCT infection.

Results

From December 2018 to December 2019, among 4,429 couples who underwent FPHC; 1,925 were pregnant, and 1,816 couples were tracked for pregnancy outcomes, including 1,471 normal pregnancies and 345 (19.00%) APOs. The rest of 109 pregnant couples did not answer the phone or refused to answer the pregnancy outcome during the follow-up. Among APOs, the number of spontaneous abortions was 122 (35.36%), the number of macrosomia was 85 (24.64%), the number of low birth weight (LBW) & preterm births (PTB) was 39 (11.30%), the number of LBW was 34 (9.86%), and the number of PTB was 31 (8.99%). The prevalence of GCT infection in females and males was 4.24% [95% Confidence Interval, (CI): 3.41-5.27%] and 3.58% (95% CI: 2.79-4.57%), respectively. More than half (52.69%, 49/93) of the couples were GCT-concordant. The prevalence of APOs in couples without GCT infection was 18.74% (332/1,772). The prevalence of APOs in female GCT-discordant was 32.14% (9/28), and the prevalence of APOs in male GCT-discordant was 25% (4/16). The prevalence of APOs in GCT-concordant was 12.24% (6/49). Multivariable analysis indicated that females 30-35 years old [adjusted Odds Ratio (aOR) = 1.08, 95% CI: 1.01-1.17] and over 35 years old (aOR = 1.16, 95% CI: 1.03-1.32) were more likely to experiencing APOs.

Conclusion

Although only women's age was found to be associated with APOs, the prevalence of APOs with GCT-discordant in couples, especially female GCT-discordant, was higher than in those without infection or who were GCT-concordant, suggesting that these groups, especially in older women, should be paid more attention to in follow-ups to improve reproductive health.

Therapeutic Options for Chlamydia trachomatis Infection: Present and Future

Sexually transmitted infections (STIs), such as Chlamydia trachomatis (Ct) infection, have serious consequences for sexual and reproductive health worldwide. Ct is one of the most common sexually transmitted bacterial infections in the world, with approximately 129 million new cases per year. C. trachomatis is an obligate intracellular Gram-negative bacterium. The infection is usually asymptomatic, notwithstanding, it could also be associated with severe sequels and complications, such as chronic pain, infertility, and gynecologic cancers, and thus there is an urgent need to adequately treat these cases in a timely manner. Consequently, beyond its individual effects, the infection also impacts the economy of the countries where it is prevalent, generating a need to consider the hypothesis of implementing Chlamydia Screening Programs, a decision that, although it is expensive to execute, is a necessary investment that unequivocally will bring financial and social long-term advantages worldwide. To detect Ct infection, there are different methodologies available. Nucleic acid amplification tests, with their high sensitivity and specificity, are currently the first-line tests for the detection of Ct. When replaced by other detection methods, there are more false negative tests, leading to underreported cases and a subsequent underestimation of Ct infection's prevalence. Ct treatment is based on antibiotic prescription, which is highly associated with drug resistance. Therefore, currently, there have been efforts in line with the development of alternative strategies to effectively treat this infection, using a drug repurposing method, as well as a natural treatment approach. In addition, researchers have also made some progress in the Ct vaccine development over the years, despite the fact that it also necessitates more studies in order to finally establish a vaccination plan. In this review, we have focused on the therapeutic options for treating Ct infection, expert recommendations, and major difficulties, while also exploring the possible avenues through which to face this issue, with novel approaches beyond those proposed by the guidelines of Health Organizations.

Chlamydia trachomatis as a Current Health Problem: Challenges and Opportunities

Chlamydia is one of the most common sexually transmitted bacterial infections (STIs) worldwide. It is caused by Chlamydia trachomatis (CT), which is an obligate intracellular bacterium. In some cases, it can occur in coinfection with other parasites, increasing the pathologic potential of the infection. The treatment is based on antibiotic prescription; notwithstanding, the infection is mostly asymptomatic, which increases the risk of transmission. Therefore, some countries have implemented Chlamydia Screening Programs in order to detect undiagnosed infections. However, in Portugal, there is no CT screening plan within the National Health Service. There is no awareness in the general healthcare about the true magnitude of this issue because most of the methods used are not Nucleic Acid Amplification Technology-based and, therefore, lack sensitivity, resulting in underreporting infection cases. CT infections are also associated with possible long-term severe injuries. In detail, persistent infection triggers an inflammatory milieu and can be related to severe sequels, such as infertility. This infection could also trigger gynecologic tumors in women, evidencing the urgent need for cost-effective screening programs worldwide in order to detect and treat these individuals adequately. In this review, we have focused on the success of an implemented screening program that has been reported in the literature, the efforts made concerning the vaccine discovery, and what is known regarding CT infection. This review supports the need for further fundamental studies in this area in order to eradicate this infection and we also suggest the implementation of a Chlamydia Screening Program in Portugal.

Despite Excellent Test Characteristics of the cobas 4800 CT/NG Assay, Detection of Oropharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae Remains Challenging

Oropharyngeal Chlamydia trachomatis (CT) infections and, especially, Neisseria gonorrhoeae (NG) infections are common, but few commercial nucleic acid amplification tests (NAATs) specify extragenital samples for intended use. The test characteristics of the cobas 4800 CT/NG assay were evaluated for oropharyngeal swabs. The technical validation included analysis of the specificity, sensitivity, dynamic range, linearity, efficiency, and precision. The probability of detection curve combined with historical data enabled the estimation of potentially missed diagnoses. A clinical evaluation was performed on a subset of 2,798 clinical samples available from routine diagnostics. Results of the cobas 4800 were compared with those from in-house C. trachomatis/N. gonorrhoeae PCR assays. Discrepant samples were tested with resolver assays, and these results were considered decisive. No cross-reactivity was seen in the analytical specificity analysis. High linearity (R ² ≥ 0.983), efficiency (89% to 99%), and precision (cycle threshold [C_T ] value of 0.1 to 0.9) were seen for both C. trachomatis and N. gonorrhoeae The limit of detection in oropharyngeal samples was 3.2 × 10² inclusion-forming units (IFU)/ml for C. trachomatis and 6.7 × 10² CFU/ml for N. gonorrhoeae Estimates on potentially missed diagnoses were up to 7.2% for C. trachomatis and up to 24.7% for N. gonorrhoeae Clinical sensitivity and specificity were evaluated with 25 C. trachomatis-positive, 86 N. gonorrhoeae-positive, and 264 negative samples, resulting in 100% and 99.6% for C. trachomatis and 100% and 96.7% for N. gonorrhoeae, respectively. The findings in this study demonstrate the utility of the cobas 4800 CT/NG assay for oropharyngeal samples. Despite its being a highly accurate test, the range of reported C_T values, especially for N. gonorrhoeae, suggests relatively low oropharyngeal loads. Hence, consistent detection over the full range of oropharyngeal loads could be impaired.

Men and Women Have Similar Neisseria gonorrhoeae Bacterial Loads: a Comparison of Three Anatomical Sites

Neisseria gonorrhoeae is a common bacterial sexually transmitted infection (STI). Currently, there are limited data on the bacterial load in both men and women and on both genital and extragenital sites. Therefore, we quantified N. gonorrhoeae bacterial loads in a large population of women, heterosexual men, and men who have sex with men (MSM) at three different anatomical sites. N. gonorrhoeae-positive samples (n = 1265) of STI clinic consultations (n = 944) were tested for N. gonorrhoeae with the Roche Cobas 4800 system, and quantification cycle (Cq) values were used as an inversely proportional measure for N. gonorrhoeae bacterial load after interpolation from a standard curve. Bacterial loads were compared between sample materials and sexes using t tests. The following mean N. gonorrhoeae loads were observed: urine, 4.5 ± 1.0 log₁₀ CFU/ml; vaginal swabs, 4.3 ± 1.1 log₁₀ CFU/ml; anorectal swabs (women), 4.0 ± 1.2 log₁₀ CFU/ml; anorectal swabs (men), 4.5 ± 1.3 log₁₀ CFU/ml; oropharyngeal swabs (women), 2.8 ± 0.9 log₁₀ CFU/ml; and oropharyngeal swabs (men), 3.2 ± 1.0 log₁₀ CFU/ml. Oropharyngeal swabs had a significantly lower N. gonorrhoeae load (P < 0.001) than genital and anorectal samples. Loads did not differ between men and women. This is the first study that determined N. gonorrhoeae load in both women and men at three anatomical sites. The substantial N. gonorrhoeae load at all sample sites suggest that all sites may have transmission potential. However, the oropharyngeal site presents the lowest bacterial load. Men and women have a similar N. gonorrhoeae loads on separate anatomical sites, arguing for similar transmission potential and similar clinical relevance.

Rapid and accurate diagnosis of Chlamydia trachomatis in the urogenital tract by a dual-gene multiplex qPCR method

Introduction. Chlamydia trachomatis (C. trachomatis, CT) is an obligatory intracellular bacterium that causes urogenital tract infections and leads to severe reproductive consequences. Therefore, a rapid and accurate detection method with high sensitivity and specificity is an urgent requirement for the routine diagnosis of C. trachomatis infections.Aim. In this study, we aimed to develop a multiplex quantitative real-time PCR (qPCR) assay based on two target regions for accurate detection of C. trachomatis in urogenital tract infections.Methodology. Primers and probes based on the conserved regions of the cryptic plasmid and 23S rRNA gene were designed. Then, two qPCR assays were established to screen for the optimal probe and primers for each of the two target regions. Subsequently, the multiplex qPCR method was developed and optimized. For the diagnostic efficiency evaluation, 1284 urogenital specimens were tested by the newly developed multiplex qPCR method, an immunological assay and a singleplex qPCR assay widely used in hospitals.Results. The multiplex qPCR method could amplify both target regions in the range of 1.0×10²-1.0×10⁸ copies ml^-1 with a strong linear relationship, and lower limits of detection (LODs) for both targets reached 2 copies PCR^-1. For the multiplex qPCR method, the diagnostic sensitivity and specificity was 100.0 % (134/134) and 99.3 % (1142/1150), respectively. For the singleplex qPCR assay, the diagnostic sensitivity and specificity was 88.8 % (119/134) and 100.0 % (1150/1150), respectively. For the immunological assay, the diagnostic sensitivity and specificity was 47.0 % (63/134) and 100.0 % (1150/1150), respectively.Conclusion. In this study, a multiplex qPCR assay with high sensitivity and specificity for rapid (≤2.0 h) and accurate diagnosis of C. trachomatis was developed. The qPCR assay has the potential to be used as a routine diagnostic method in clinical microbiology laboratories.

Prevalence, risk factors, and medical costs of Chlamydia trachomatis infections in Shandong Province, China: a population-based, cross-sectional study

Background

A population-based study of Chlamydia trachomatis (CT) infections is essential in designing a specific control program; however, no large investigation of CT infections among the general population in mainland China has been conducted since 2000. We aimed to determine the prevalence, risk factors, and associated medical costs of CT among residents, 18–49 years of age, in Shandong, China.

Methods

From May to August 2016, a multistage probability sampling survey involving 8074 individuals was distributed. Data were collected via face-to-face interviews, followed by self-administered questionnaire surveys. First-void urines were collected and tested for CT and Neisseria gonorrhoeae (NG) using nucleic acid amplification.

Results

The weighted prevalence of CT infection was 2.3% (95% confidence interval [CI], 1.5–3.2) in females and 2.7% (1.6–3.8) in males. Women, 30–34 years of age, had the highest prevalence of CT infections (3.5%, 2.6–4.4), while the highest prevalence of CT infections in males was in those 18–24 years of age (4.3%, 0.0–8.8). Neisseria gonorrhoeae infection had a prevalence of 0.1% (0.0–0.3) in women and 0.03% (0.0–0.1) in men. Risk factors for CT infections among females included being unmarried, divorced, or widowed (odds ratio [OR], 95% CI 3.57, 1.54–8.24) and having two or more lifetime sex partners (3.72, 1.14–12.16). Among males, first intercourse before 20 years of age (1.83, 1.10–3.02) and having two or more lifetime sex partners (1.85, 1.14–3.02) were associated with CT infections. The estimated lifetime cost of CT infections in patients 18–49 years of age in Shandong was 273 million (range, 172–374 million) China Renminbi in 2016.

Conclusions

This study demonstrated a high burden of CT infections among females < 35 years of age and males < 25 years of age in Shandong. Thus, a CT infection control program should focus on this population, as well as others with identified risk factors.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3432-y) contains supplementary material, which is available to authorized users.

Usefulness of a novel multiplex real-time PCR assay for the diagnosis of sexually-transmitted infections

INTRODUCTION

Sexually transmitted infections (STI) are currently on the increase worldwide. New molecular tools have been developed in the past few years in order to improve their diagnosis. An evaluation was carried out using a new commercially available real-time PCR assay, Anyplex™ II STI-7 (Seegene, Seoul, Korea), which detects seven major pathogens in a single reaction - Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, and Ureaplasma parvum - and compared with conventional methods performed in our laboratory.

MATERIALS AND METHODS

Two different populations were included, and 267 specimens from different sites of infection (urines, endocervical swabs, rectal swabs, vaginal swabs, urethral swabs and one inguinal adenopathy) were processed for both methods.

RESULTS

The parameters of clinical performance were calculated for C. trachomatis, N. gonorrhoeae, and T. vaginalis, and the assay achieved sensitivities (SE) from 93.94% to 100%, and specificities (SP) from 96.55% to 100%, with negative predictive values (NPV) from 93.33% to 98.85%, and positive predictive values (PPV) from 96.88% to 100%, with a very good agreement (kappa index from 0.88 to 1).

CONCLUSIONS

Anyplex™ II STI-7 is a good tool for the reliable diagnosis of STI. Its ease of use and processing allows it to be incorporated into the day to day laboratory work.

Performance of the NG OligoGen kit for the diagnosis of Neisseria gonorrhoeae: comparison with cobas 4800 assay

PCR assays are nowadays between the most sensitive and reliable methods for screening and diagnosing sexually transmitted infections (STIs). The aim of this study was to analyze the reliability, accuracy, and usefulness of the new NG OligoGen kit in comparison with the cobas 4800 assay for the detection of Neisseria gonorrhoeae in clinical samples. A prospective study was designed for detection of N. gonorrhoeae including urine samples (n=152), rectal (n=80), endocervical (n=67), pharyngeal (n=41), and urethral swabs (n=5) that were sent from a regional STI clinic in Seville, Spain. Samples were collected from 255 (73.9%) men and 90 women. Sensitivity, specificity, positive and negative predicative values, and kappa value for N. gonorrhoeae detection using the NG OligoGen kit were 99.6%, 100%, 100%, 99.1%, and 0.99, respectively. Statistical data obtained in this study confirm the usefulness and reliable results of this new assay.

Evaluation of a dilution method for non-evaluable results in the detection of Chlamydia trachomatis and Neisseria gonorrhoeae with the Cobas 4800 platform

INTRODUCTION

A variable percentage of samples analysed using the Cobas 4800 assay can give an invalid result by PCR inhibition or erroneous due to incorrect DNA extraction with the Cobas 4800 CT/NG test.

METHOD

An analysis was performed using the vortex agitation and dilution protocol on the original sample (swab or urine) for a total of 116 samples. In order to analyse the sensitivity of this method, 100 samples (swabs and urine) with known results were retested.

RESULTS

A total of 98.3% (114/116) of the samples analysed were resolved with this protocol with 100% agreement after reviewing clinical data, Gram stain, and other samples analysed in parallel from the same patient.

DISCUSSION

The data indicate no loss of sensitivity with this protocol; thus Cobas 4800 users could use this method without the need for alternative methods.

Comparison of the CT OligoGen kit with cobas 4800 assay for detection of Chlamydia trachomatis

INTRODUCTION

A prospective study was designed to assess the performance of the new CT OligoGen kit and the cobas 4800 assay for detection of Chlamydia trachomatis.

METHODS

A set of samples that included urine samples (n=212), endocervical (n=167), rectal (n=53), pharyngeal (n=7) and urethral swabs (n=3). The samples were sent from a regional sexually transmitted diseases (STD) clinic in Seville, Spain, and were collected from 261 men and 181 women. Discordant results were re-analyzed and clinical data and other tests were reviewed in order to resolve them.

RESULTS

Sensitivity, specificity, positive predicative value (PPV), negative predictive value (NPV) and kappa value for C. trachomatis detection using the CT OligoGen kit were 98.5%, 100%, 100%, 95.4% and 0.97, respectively.

CONCLUSIONS

This new kit had a high sensitivity, specificity, PPV and NPV for C. trachomatis, therefore the performance profile confirms the usefulness and reliable results of this new assay.

Evaluation of the Versant CT/GC DNA 1.0 assay (kPCR) for the detection of extra-genital Chlamydia trachomatis and Neisseria gonorrhoeae infections

Screening for extra-genital Chlamydia trachomatis and Neisseria gonorrhoeae infections is a crucial component for sexually transmitted diseases management, even if at present days no commercial methods have been approved for use on pharyngeal and rectal specimens by the US FDA or have received the conformity CE marking. Here we report the analytical sensitivities of the Versant CT/GC 1.0 assay (Siemens Healthcare Diagnostics, Tarrytown, NY, USA) on rectal and pharyngeal swabs, and an evaluation about the suitability for this assay with two widely used swab collection devices (E-Swab and eNAT, Copan, Brescia, Italy). The limits of detection for rectal and pharyngeal specimens with the Versant assay were 10 copies/ml and 1.0 copies/ml, for C. trachomatis and N. gonorrhoeae, respectively. False positive results due to the presence of non-gonococcal Neisseria species were excluded when clinical rectal and pharyngeal samples containing organisms identified as N. meningitidis, N. sicca, N. flavescens and N. subflava were tested. Due to its sensitivity and specificity, the Versant assay represents a good choice for the diagnosis of chlamydial and/or gonococcal infections not only in genito-urinary samples, but also on rectal and pharyngeal swabs.

Comparison of urine and cervical samples for detecting human papillomavirus (HPV) with the Cobas 4800 HPV test

BACKGROUND

Human papillomavirus (HPV) is the main cause of cervical cancer. The development of non-invasive self-sample collection methods would have the potential advantage of increasing the acceptance of the screening procedures.

OBJECTIVES

To compare human papillomavirus (HPV) DNA detection and genotyping with the Cobas 4800 HPV test (Roche Diagnostic, Spain) on paired cervical and first voided urine.

STUDY DESIGN

Paired urine and cervical samples were collected from 125 women referred for evaluation of abnormal Pap smear results.

RESULTS

The overall percent agreement between HPV detection in urine and cervical samples was 88%. A substantial concordance rate of HPV DNA detection in both samples was observed (κ=0.76; 95% IC: 64-87). In this high prevalence population the sensitivity, specificity, NPV and PPV for detection of HPV DNA from urine versus cervical samples were 90.5% (95% IC: 80-95%), 85%, (95% IC: 74-92%), 89.8% (95% IC: 79.5-95.3) and 86.4% (95% IC: 76.1-92.7) respectively. Compared to histologically confirmed CIN 2/3 disease, the clinical sensitivity and specificity for the detection of high-risk HPV in urine samples were 95% (95% IC: 76-97%) and 52.4% (95% IC: 40-64%) respectively.

CONCLUSIONS

These results suggest that urine samples processed with Cobas 4800 HPV test may be useful for clinical management of HPV infection.

A misleading urethral smear with polymorphonuclear leucocytes and intracellular diplococci; case report of urethritis caused by Neisseria meningitidis

The primary pathogens found in men with urethritis are Chlamydia trachomatis and Neisseria gonorrhoeae. Rapid diagnosis of N. gonorrhoeae infection can be made based on a Gram- or methylene blue-stained urethral smear. We describe a case of a man with purulent penile discharge, in which microscopic examination led to the presumptive diagnosis of gonorrhoea. A nucleic acid amplification test was negative for N. gonorrhoeae but positive for C. trachomatis. Culture showed Gram-negative diplococci which were identified as Neisseria meningitidis. N. meningitidis can be sporadically pathogenic in the genito-urinary tract and mimicks gonococcal urethritis, and appears identical by microscopy. When a gonococcal urethritis is suspected based on clinical signs and microscopic examination, but investigatory tests cannot confirm the diagnosis, a N. meningitidis infection should be considered.

Cobas® 4800: a fully automated system for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae

Chlamydia trachomatis and Neisseria gonorrhoeae (CT/NG) are the most common sexually transmitted bacterial infections globally and account for the majority of the infections monitored by public health surveillance systems. Therefore, access to diagnostic tools that facilitate identification of these infections is critical to sexually transmitted infection control efforts. The cobas(®) 4800 system is a fully automated system that incorporates nucleic acid extraction and real-time PCR. The cobas 4800 CT/NG assay is one component of the test menu available on this system. The cobas 4800 CT/NG assay has excellent sensitivity and specificity as a result of dual primer targets, it utilizes self-obtained sample types, and is only one assay in a larger menu of tests that are performed on a system that is easy to use and maintain.

Neisseria gonorrhoeae false-positive result obtained from a pharyngeal swab by using the Roche cobas 4800 CT/NG assay in New Zealand in 2012

The Roche cobas 4800 CT/NG assay is a commonly used commercial system for screening for Neisseria gonorrhoeae infection, and previous studies have shown the method to be highly sensitive and specific for urogenital samples. We present the first confirmed clinical N. gonorrhoeae false-positive result using the cobas 4800 NG assay, obtained from testing a pharyngeal swab sample and caused by cross-reaction with a commensal Neisseria strain.

A multiplexed microfluidic PCR assay for sensitive and specific point-of-care detection of Chlamydia trachomatis

BACKGROUND

Chlamydia trachomatis (Ct) is the most common cause of bacterial sexually transmitted diseases (STD) worldwide. While commercial nucleic acid amplification tests (NAAT) are available for Ct, none are rapid or inexpensive enough to be used at the point-of-care (POC). Towards the first Ct POC NAAT, we developed a microfluidic assay that simultaneously interrogates nine Ct loci in 20 minutes.

METHODOLOGY AND PRINCIPAL FINDINGS

Endocervical samples were selected from 263 women at high risk for Ct STDs (∼35% prevalence). A head-to-head comparison was performed with the Roche-Amplicor NAAT. 129 (49.0%) and 88 (33.5%) samples were positive by multiplex and Amplicor assays, respectively. Sequencing resolved 71 discrepant samples, confirming 53 of 53 positive multiplex samples and 12 of 18 positive Amplicor samples. The sensitivity and specificity were 91.5% and 100%, and 62.4% and 95.9%, respectively, for multiplex and Amplicor assays. Positive and negative predictive values were 100% and 91%, and 94.1% and 68.6%, respectively.

CONCLUSIONS

This is the first rapid multiplex approach to Ct detection, and the assay was also found to be superior to a commercial NAAT. In effect, nine simultaneous reactions significantly increased sensitivity and specificity. Our assay can potentially increase Ct detection in globally diverse clinical settings at the POC.