Evaluation of three automated nucleic acid amplification systems for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in first-void urine specimens

Relative Cost and Infectious Days Averted Associated With Rapid Gonorrhea and Chlamydia Testing Among Men Who Have Sex With Men

BACKGROUND

Standard-of-care nucleic acid amplification tests (routine NAATs) for Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) can take several days to result and therefore delay treatment. Rapid point-of-care GC/CT NAAT (rapid NAAT) could reduce the time to treatment and therefore onward transmission. This study evaluated the incremental cost per infectious day averted and overall cost of implementation associated with rapid compared with routine NAAT.

METHODS

Prospective sexually transmitted infection (STI) treatment data from men who have sex with men and transgender women in San Diego who received rapid NAAT between November 2018 and February 2021 were evaluated. Historical time from testing to treatment for routine NAAT was abstracted from the literature. Costs per test for rapid and routine NAAT were calculated using a micro-costing approach. The incremental cost per infectious day averted comparing rapid to routine NAAT and the costs of rapid GC/CT NAAT implementation in San Diego Public Health STI clinics were calculated.

RESULTS

Overall, 2333 individuals underwent rapid NAAT with a median time from sample collection to treatment of 2 days compared with 7 to 14 days for routine NAAT equating to a reduction of 5 to 12 days. The cost of rapid and routine GC/CT NAAT was $57.86 and $18.38 per test, respectively, with a cost-effectiveness of between $2.43 and $5.82 per infectious day averted. The incremental cost of rapid NAAT improved when at least 2000 tests were performed annually.

CONCLUSIONS

Although rapid GC/CT NAAT is more expensive than routine testing, the reduction of infectious days between testing and treatment may reduce transmission and provide improved STI treatment services to patients.

Comparison between Aptima® assays (Hologic) and the CoBAS® 6800 system (Roche) for the diagnosis of sexually transmitted infections caused by Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium

Nowadays, it is of utmost importance to use fully validated assays for molecular-based diagnosis. In the field of sexually transmitted disease (STD), Roche and Hologic provide assays for diagnosing Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium (MG), and Trichomonas vaginalis (TV). A total of 212 clinical samples were tested. Aptima® Combo 2 (detecting CT and NG), Aptima® M. genitalium and the Aptima® T. vaginalis on the Panther® system were compared to CoBAS® CT/NG and CoBAS® TV/MG running on the CoBAS® 6800 system. To solve the discrepancies, Allplex™ STI Essential assay (Seegene®) and/or Sanger DNA sequencing were used. The diagnostic performance was calculated by mean of the sensitivity and specificity parameters. Aptima® (sensitivity: 98.90%, specificity: 100%), CoBAS® (sensitivity 100%, specificity: 96.67%). The CoBAS® combo (CT/NG) failed detecting NG from an anal/rectum specimen, which is not included into the validated specimens of the assay. Aptima® combo 2 produced two false positives (CT and NG), not detected by the third tests. All the assays showed an optimal diagnostic capacity, meeting the requirements for IVD DNA-based assays. All products work optimally on automatic platforms, minimizing time and risk of contamination during handling.

A profile of the FDA-approved and CE/IVD-marked Aptima Mycoplasma genitalium assay (Hologic) and key priorities in the management of M. genitalium infections

INTRODUCTION

Mycoplasma genitalium (MG) causes frequently asymptomatic STIs. MG prevalence figures are lacking and management is complicated by the lack of etiological diagnostics and high antimicrobial resistance in many countries. Appropriately validated, quality-assured, and FDA-approved MG diagnostic assays have been lacking.

AREAS COVERED

The clinical and analytical performance characteristics of the Aptima® MG assay, the first FDA-approved MG nucleic acid amplification test (NAAT), are summarized. Key priorities in the management and control of MG infections are also discussed.

EXPERT OPINION

Highly sensitive, specific, and quality-assured MG NAATs, e.g. the Aptima MG assay on the automated and flexible Panther® platform, are imperative to improve the management and control of MG infections internationally. This testing, combined with macrolide-resistance testing (not yet available on the Panther platform), offers a rapid, high-throughput, and appropriate diagnosis of MG. Macrolide resistance-guided sequential treatment needs to be implemented for MG infections. Dual antimicrobial therapy, novel antimicrobials and, ideally, a vaccine may become essential.

Detection of sexually transmitted disease-causing pathogens from direct clinical specimens with the multiplex PCR-based STD Direct Flow Chip Kit

Pathogens causing sexually transmitted diseases (STDs) include viruses, bacteria, and parasites. The ability to rapidly and efficiently detect these pathogens in a single reaction still remains a health challenge. The aim of this study was to evaluate the clinical reliability and accuracy of the STD Direct Flow Chip Kit (Vitro, IVD-EC approved), which can simultaneously detect up to 9 different species of STD pathogens at once. This kit enables direct analysis-direct-PCR-of clinical specimens (urine, semen, endocervical, urethral, nasopharyngeal, and perianal swabs) without DNA purification for the following pathogens: Chlamydia trachomatis (serovars A-K and L1-L3), Haemophilus ducreyi, Herpes Simplex Virus (Types I and II), Mycoplasma genitalium, Mycoplasma hominis, Neisseria gonorrhoeae, Treponema pallidum, Trichomonas vaginalis, and Ureaplasma. The Anyplex™ II STI-7 Detection Kit (Seegene, IVD-EC) was used as the reference's method. Existing discordances were resolved using either a third molecular assay or DNA sequencing. Clinical performance was evaluated at two different stages: (i) from purified DNA of three hundred and fifty-eight clinical specimens with a diagnostic sensitivity (SE) and specificity (SP) of 99.4% and 100%, respectively, and an agreement of 99% (kappa index, κ = 0.97) with the reference's method and; (ii) by direct-PCR from six hundred and thirty-three specimens rendering SE, SP, and agreement values of 98.4%, 99.9%, and 98.0% (κ = 0.95), respectively. The STD Direct Flow Chip Kit constitutes a promising alternative to routine procedures in diagnostic, allowing direct analysis of specimens and enabling the detection of a broad panel of pathogens.

Gonorrhoea

The bacterium Neisseria gonorrhoeae causes the sexually transmitted infection (STI) gonorrhoea, which has an estimated global annual incidence of 86.9 million adults. Gonorrhoea can present as urethritis in men, cervicitis or urethritis in women, and in extragenital sites (pharynx, rectum, conjunctiva and, rarely, systemically) in both sexes. Confirmation of diagnosis requires microscopy of Gram-stained samples, bacterial culture or nucleic acid amplification tests. As no gonococcal vaccine is available, prevention relies on promoting safe sexual behaviours and reducing STI-associated stigma, which hinders timely diagnosis and treatment thereby increasing transmission. Single-dose systemic therapy (usually injectable ceftriaxone plus oral azithromycin) is the recommended first-line treatment. However, a major public health concern globally is that N. gonorrhoeae is evolving high levels of antimicrobial resistance (AMR), which threatens the effectiveness of the available gonorrhoea treatments. Improved global surveillance of the emergence, evolution, fitness, and geographical and temporal spread of AMR in N. gonorrhoeae, and improved understanding of the pharmacokinetics and pharmacodynamics for current and future antimicrobials in the treatment of urogenital and extragenital gonorrhoea, are essential to inform treatment guidelines. Key priorities for gonorrhoea control include strengthening prevention, early diagnosis, and treatment of patients and their partners; decreasing stigma; expanding surveillance of AMR and treatment failures; and promoting responsible antimicrobial use and stewardship. To achieve these goals, the development of rapid and affordable point-of-care diagnostic tests that can simultaneously detect AMR, novel therapeutic antimicrobials and gonococcal vaccine(s) in particular is crucial.

Comparison between Aptima Assays (Hologic) and the Allplex STI Essential Assay (Seegene) for the diagnosis of Sexually transmitted infections

Sexually transmitted infections (STIs) remain a worldwide problem and a severe threat to public health. The purpose of this study was to compare Aptima^® Assays (Hologic^®) and the Allplex^™ STI Essential Assay (Seegene^®) for the simultaneous detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis and Mycoplasma genitalium in clinical practice. The Aptima^® assays (Hologic^®) are based on a transcription-mediated amplification (TMA) method. The Allplex^™ STI Essential assay (Seegene^®) is based on a multiplex Real-Time PCR (RT-PCR) method. A total of 622 clinical samples from different anatomical sites were tested using both methods. A total of 88 (14.1%) and 66 (10.6%) positive samples were found for any of the TMA assays used and for the RT-PCR assay, respectively. Aptima^® assays showed a slightly higher rate of positive results for all pathogens except for T. vaginalis, the results of which were similar to those obtained with Allplex^™. The most commonly detected pathogen was C. trachomatis (37 samples; 5.9% using TMA assays) and the anatomical site with the highest prevalence of microorganisms was a non-urogenital site, the pharynx (27 positive samples; 4.3%). Using the Aptima^® assays as reference method, the comparison showed that the average specificity of multiplex RT-PCR was 100.0% for the four pathogens. However an average sensitivity of 74.5% was observed, showing 95.2% (CI95%; 93.6–96.9) of overall concordance (κ = 0.80). In conclusion, the Aptima^® assays show a higher sensitivity on a wide range of sample types compared to the Allplex^™ assay.

Comparison of Workflow, Maintenance, and Consumables in the GeneXpert Infinity 80 and Panther Instruments While Testing for Chlamydia trachomatis and Neisseria gonorrhoeae

BACKGROUND

The 2015 Sexually Transmitted Diseases Treatment Guidelines from the Centers for Disease Control and Prevention recommend testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using nucleic acid amplification tests, and prompt treatment of infected persons on site under direct observation. Faster time to results may enable treatment and management outcomes.

METHODS

Workflow parameters for processing 1, 10, 48, 96, and 192 tests were determined in the GeneXpert Infinity 80 (Cepheid) and Panther (Hologic) instruments.

RESULTS

In an Xpert CT/NG cartridge, the time to first results on the Infinity 80 was 1 hour 30 minutes for single or multiple tests and final results for 10, 48, 96, and 192 tests were available at 1 hour 37 minutes, 1 hour 54 minutes, 3 hour 17 minutes, and 5 hour 7 minutes, respectively. With the Aptima CT/GC assay on the Panther, the respective times were 3 hr 45 min for the first test result, and 3 hour 51 minutes, 4 hour 38 minutes, 5 hour 26 minutes, and 7 hour 4 minutes to final results. The Panther required more time for maintenance and consumed a greater variety of plastics and reagents but required less hands-on time when testing larger numbers of specimens.

CONCLUSIONS

The Infinity 80 is a versatile instrument for continuous random access testing of small or large numbers of clinical specimens and may provide diagnostic results, in some settings, in time for treatment of CT and NG infections.

Comparison of cobas 4800, m2000, Viper XTR, and Infinity 80 Automated Instruments When Processing Urine Specimens for the Diagnosis of Chlamydia trachomatis and Neisseria gonorrhoeae

OBJECTIVES

North American and European advisory groups recommend testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) with nucleic acid amplification tests. Testing is often performed on automated instruments. The objectives of this study were to process urines for the diagnosis of CT and NG and to examine workflow procedures and outcomes.

METHODS

While processing 1, 24, 48, 96, and 192 urine specimens on 3 batch-mode systems which use 96-well plates: cobas 4800, m2000, and Viper XTR and the random access cartridge testing GeneXpert Infinity 80, we measured assay performance, hands-on time for processing and maintenance, reagents and plastics consumption, time required to obtain results, and testing accuracy.

RESULTS

The Infinity 80 required the least hands-on time for single specimens and smaller batches, whereas the Viper XTR and m2000 required the most hands-on time for all batch sizes. Cumulative daily, weekly, and monthly maintenance was highest for the Viper XTR and lowest for Infinity 80. All batch-mode instruments consumed large amounts of disposables. Time to results was shortest for the Infinity 80, and the Viper XTR provided the shortest time for the batch-mode instruments. All systems showed similar diagnostic accuracy.

CONCLUSIONS

Because detection performances were similar, issues of hands-on time, maintenance, time to results, and consumables are important operational factors for the diagnosis and treatment of CT/NG infections.

Diagnostic Procedures to Detect Chlamydia trachomatis Infections

The intracellular life style of chlamydia and the ability to cause persistent infections with low-grade replication requires tests with high analytical sensitivity to directly detect C. trachomatis (CT) in medical samples. Nucleic acid amplification tests (NAATs) are the most sensitive assays with a specificity similar to cell culture and are considered the method of choice for CT detection. In addition, NAATs can be performed on various clinical specimens that do not depend on specific transport and storage conditions, since NAATs do not require infectious bacteria. In the case of lower genital tract infections, first void urine and vaginal swabs are the recommended specimens for testing males and females, respectively. Infections of anorectal, oropharyngeal and ocular epithelia should also be tested by NAAT analysis of corresponding mucosal swabs. In particular, anorectal infections of men who have sex with men (MSM) should include evaluation of lymphogranuloma venereum (LGV) by identification of genotypes L1, L2 or L3. Detection of CT antigens by enzyme immunoassay (EIAs) or rapid diagnostic tests (RDTs) are unsuitable due to insufficient sensitivity and specificity. Recent PCR-based RDTs, however, are non-inferior to standard NAATs, and might be used at the point-of-care. Serology finds application in the diagnostic work-up of suspected chronic CT infection but is inappropriate to diagnose acute infections.

Evaluation of the new AmpliSens multiplex real-time PCR assay for simultaneous detection of Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, and Trichomonas vaginalis

In this study, we performed an evaluation of the new CE-marked multiplex real-time AmpliSens N.gonorrhoeae/C.trachomatis/M.genitalium/T.vaginalis-MULTIPRIME-FRT PCR assay compared to APTIMA tests, i.e., APTIMA COMBO 2 assay, APTIMA Trichomonas vaginalis assay (FDA-approved), and two different APTIMA Mycoplasma genitalium assays (research use only; one of them only used for discrepancy analysis). Vaginal swabs (n = 209) and first-void urine (FVU) specimens from females (n = 498) and males (n = 554), consecutive attendees (n = 1261) at a dermatovenerological clinic in Sweden, were examined. The sensitivity of the AmpliSens PCR assay for detection of C. trachomatis (6.3% prevalence), M. genitalium (5.7% prevalence), N. gonorrhoeae (0.3% prevalence), and T. vaginalis (0.08% prevalence) was 97.5% (95% confidence interval (CI): 91.2-99.6%), 81.9% (95% CI: 70.7-89.7%), 100% (95% CI: 40.2-100%) and 100% (95% CI: 16.5-100%), respectively. The specificity of the AmpliSens PCR assay was 100% (95% CI: 99.6-100%) for all agents. The analytical sensitivity and specificity for N. gonorrhoeae detection was excellent, i.e., 55 international gonococcal strains detected and 135 isolates of 13 non-gonococcal Neisseria species were negative. In conclusion, the multiplex real-time AmpliSens N.gonorrhoeae/C.trachomatis/M.genitalium/T.vaginalis-MULTIPRIME-FRT PCR assay demonstrated high sensitivity and excellent specificity for the detection of C. trachomatis, N. gonorrhoeae, and T. vaginalis, and excellent specificity but suboptimal sensitivity for M. genitalium detection.

Workflow and maintenance characteristics of five automated laboratory instruments for the diagnosis of sexually transmitted infections

The choice of a suitable automated system for a diagnostic laboratory depends on various factors. Comparative workflow studies provide quantifiable and objective metrics to determine hands-on time during specimen handling and processing, reagent preparation, return visits and maintenance, and test turnaround time and throughput. Using objective time study techniques, workflow characteristics for processing 96 and 192 tests were determined on m2000 RealTime (Abbott Molecular), Viper XTR (Becton Dickinson), cobas 4800 (Roche Molecular Diagnostics), Tigris (Hologic Gen-Probe), and Panther (Hologic Gen-Probe) platforms using second-generation assays for Chlamydia trachomatis and Neisseria gonorrhoeae. A combination of operational and maintenance steps requiring manual labor showed that Panther had the shortest overall hands-on times and Viper XTR the longest. Both Panther and Tigris showed greater efficiency whether 96 or 192 tests were processed. Viper XTR and Panther had the shortest times to results and m2000 RealTime the longest. Sample preparation and loading time was the shortest for Panther and longest for cobas 4800. Mandatory return visits were required only for m2000 RealTime and cobas 4800 when 96 tests were processed, and both required substantially more hands-on time than the other systems due to increased numbers of return visits when 192 tests were processed. These results show that there are substantial differences in the amount of labor required to operate each system. Assay performance, instrumentation, testing capacity, workflow, maintenance, and reagent costs should be considered in choosing a system.

Evaluation of the Hologic gen-probe PANTHER, APTIMA Combo 2 assay in a tertiary care teaching hospital

OBJECTIVES

To evaluate the performance of the Hologic Gen-Probe (San Diego, CA) PANTHER system.

METHODS

The performance of PANTHER was compared with the Hologic Gen-Probe TIGRIS and/or Roche (Indianapolis, IN) COBAS AMPLICOR systems through testing of patient specimens and the spiked-urine matrix.

RESULTS

After discrepant resolution, PANTHER demonstrated a 99.3% (95% confidence interval [CI], 96.0%-99.9%) positive and 100% (98.5%-100.0%) negative agreement for Chlamydia trachomatis (CT) and 100% (96.6%-100.0%) positive and 100% (98.6%-100.0%) negative agreement for Neisseria gonorrhoeae (NG) for all male, female, unsexed, and NG-spiked female urine specimens combined. For other specimen types collectively, the PANTHER demonstrated 100% (95% CI, 90.6%-100.0%) positive and 100% (88.3%-100.0%) negative agreement for CT and 90.9% (62.8%-98.4%) positive and 100% (93.5%-100.0%) negative agreement for NG. Analytical sensitivity of the PANTHER in urine matrix was similar to the TIGRIS system.

CONCLUSIONS

The PANTHER system provides an excellent new addition to options for detecting CT and NG, is appropriate for testing urine samples, and will facilitate high-throughput testing in the clinical laboratory.

Time-Motion Analysis of Four Automated Systems for the Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Nucleic Acid Amplification Testing

Next-generation diagnostics for Chlamydia trachomatis and Neisseria gonorrhoeae are available on semi- or fully-automated platforms. These systems require less hands-on time than older platforms and are user friendly. Four automated systems, the ABBOTT m2000 system, Becton Dickinson Viper System with XTR Technology, Gen-Probe Tigris DTS system, and Roche cobas 4800 system, were evaluated for total run time, hands-on time, and walk-away time. All of the systems evaluated in this time-motion study were able to complete a diagnostic test run within an 8-h work shift, instrument setup and operation were straightforward and uncomplicated, and walk-away time ranged from approximately 90 to 270 min in a head-to-head comparison of each system. All of the automated systems provide technical staff with increased time to perform other tasks during the run, offer easy expansion of the diagnostic test menu, and have the ability to increase specimen throughput.

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.

Comparison of the BD Viper System with XTR Technology to the Gen-Probe APTIMA COMBO 2 Assay using the TIGRIS DTS system for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine specimens

BACKGROUND

Performances of the BD ProbeTec Chlamydia trachomatis (CT)/Neisseria Gonorrhoeae (GC) Q(x) Amplified DNA Assay reagents on a BD Viper System with XTR Technology and APTIMA COMBO 2 Assay reagents on a TIGRIS DTS platform, for detection of both CT and GC were compared.

METHODS

A total of 1018 first-void urine specimens were tested for the presence of CT and GC DNA using the 2 assays.

RESULTS

CT was detected in 143 specimens (14%). Eight specimens exhibited discordant results, and they were divided equally between the 2 assays. Based on the original results, the overall agreement for CT was 99.2%, with 97.1% and 99.5% in agreement with positive and negative specimens, respectively. Cohen's Kappa was 0.967. GC was detected in 27 specimens (2.6%). Two specimens exhibited discordant results, and they were divided equally between the 2 assays. Based on the original results, the overall agreement was 99.8%, with 96.2% and 99.9% in agreement for positive and negative specimens, respectively. Cohen's Kappa was 0.961.

CONCLUSIONS

There was a high level of agreement between the systems for both CT and GC detection.

Three-year history of transcription-mediated amplification-based Trichomonas vaginalis analyte-specific reagent testing in a subacute care patient population

A total of 7,899 specimens submitted for live clinical Trichomonas vaginalis analyte-specific reagent (ASR) screening from 2008 to 2010 were audited on the basis of patient gender, specimen source, molecular Neisseria gonorrhoeae and Chlamydia trachomatis results, and relative light unit (RLU) data yielded by T. vaginalis ASR. Only 1.4% of the screening was ordered by emergency department clinicians. The screening volume in 2010 was 126% higher than that in 2008. The proportions of annual female and male screening remained consistent throughout the 3-year interval (∼92 and 8%, respectively). Although 71.8 and 9.5% of screening was performed on endocervical and vaginal specimens, respectively, over the 3-year period, no significant difference was noted in the T. vaginalis detection rates (8.9 and 8.6%, P = 0.85). Increased T. vaginalis detection was derived from female urine specimens (12.6%) compared to female genital swabs (P = 0.0004). The proportion of female urine screening increased during the 3-year interval (P < 0.0002). T. vaginalis detection rate in males was 6.6%, with no difference between urethral and urine T. vaginalis detection (P = 0.53). The mean RLU value for 714 positive specimens was 3,971,441; analogous values for each female specimen source and combined male source testing showed no variance (P ≥ 0.29). Combined-gender T. vaginalis detection rate (9.1%) was significantly greater than those of C. trachomatis (5.9%) and N. gonorrhoeae (1.5%; P < 0.0002). Equivocal results presented at a rate of 0.4%. T. vaginalis ASR is an increasingly utilized assay that yields higher detection rates than other sexually transmitted infection etiologies in this community subacute care setting.

Molecular Diagnosis of Sexually Transmitted Chlamydia trachomatis in the United States

Chlamydia, with its Chlamydia trachomatis etiology, is the most common bacterial sexually transmitted infection in the United States and is often transmitted via asymptomatic individuals. This review summarizes traditional and molecular-based diagnostic modalities specific to C. trachomatis. Several commercially available, FDA-approved molecular methods to diagnose urogenital C. trachomatis infection include nucleic acid hybridization, signal amplification, polymerase chain reaction, strand displacement amplification, and transcription-mediated amplification. Molecular-based methods are rapid and reliable genital specimen screening measures, especially when applied to areas of high disease prevalence. However, clinical and analytical sensitivity for some commercial systems decreases dramatically when testing urine samples. In vitro experiments and clinical data suggest that transcription-mediated amplification has greater analytical sensitivity than the other molecular-based methods currently available. This difference may be further exhibited in testing of extragenital specimens from at-risk patient demographics. The development of future molecular testing could address conundrums associated with confirmatory testing, medicolegal testing, and test of cure.

2010 European guideline for the management of Chlamydia trachomatis infections

This guideline aims to provide comprehensive information regarding the management of infections caused by Chlamydia trachomatis in European countries. The recommendations contain important information for physicians and laboratory staff working with sexually transmitted infections (STIs) and/or STI-related issues. Individual European countries may be required to make minor national adjustments to this guideline as some of the tests or specific local data may not be accessible, or because of specific laws.

[Usefulness of real-time PCR in detecting Chlamydia trachomatis and Neisseria gonorrhoeae in endocervical swabs and first-voided urine specimens]

We evaluated performance of Abbott RealTime CT/NG assay (real-time PCR, Abbott Japan) for detect Chlamydia trachomatis and Neisseria gonorrhoeae by real-time PCR in 88 female patients with cervicitis symptoms seen at gynecological clinics and 100 male patients with urethritis symptoms seen at urological or dermatology clinics in Kitakyushu, Japan. Endocervical swab and first-voided urine (FVU) specimens were then collected from women and FVU specimens from men. Detection rates of C. trachomatis and N. gonorrhoeae by real-time PCR in the 3 types of specimens were compared to those by ProbeTec ET assay (ProbeTec, BD Diagnostic System). The overall positive concordance between real-time PCR and ProbTec were 97.1% (66/68) for C. trachomatis and 100% (33/33) for N. gonorrhoeae, C. trachomatis detection yielded 3 discordant results in endocervical specimens and 1 discordant result in male FVU by real-time PCR and ProbTec. Three of 4 reexamined using Aptime Combo 2 Assay (Fuji Rebio Inc.) were positive for C. trachomatis. Endocervical swab and FVU specimen results for C. trachomatis were discordant in 3 cases in real-time PCR and 4 in ProbeTec. Subjects with 2 or more positive endocervical awab results in female or male FVU specimens were assumed to be "true positive" for C. trachomatis. The sensitivities of real-time PCR for detecting C. trachomatis was 94.4% in endocervical swabs, 77.8% in female FVU and 97.4% in the male FVU. The sensitivities for real-time PCR for detecting N. gonorrhoeae was 100% in all 3 specimentypes. Abbott RealTime CT/NG assay was useful for detecting C. trachomatis using endocervical swabs or male FVU specimens and for detecting N. gonorrhoeae using endocervical swabs and all FVU specimens.

Evaluation of the Abbott RealTime CT/NG assay in comparison to the Roche Cobas Amplicor CT/NG assay

Several commercial methods exist for the molecular detection of Chlamydia trachomatis and Neisseria gonorrhoeae in clinical samples. Here we evaluated the performance characteristics of the newly FDA-cleared Abbott RealTime CT/NG assay (where "CT" stands for Chlamydia trachomatis and "NG" stands for Neisseria gonorrhoeae) that uses the automated m2000 molecular platform. Results were compared to those of the Roche Cobas Amplicor CT/NG assay. A total of 926 cervical swab, 45 female urine, 6 male urethral swab, and 407 male urine specimens from 1,384 patients were examined. After resolving all Roche N. gonorrhoeae-positive results with two additional real-time PCR assays, we found that the agreement between the assays was excellent. For urine samples, there was 99.6% positive agreement and 97.7% negative agreement for C. trachomatis, and for male urine samples, there was 100% positive agreement and 99.7% negative agreement for N. gonorrhoeae. For cervical swab samples, there was 98.8% positive agreement and 98.5% negative agreement for C. trachomatis, and there was 96.6% positive agreement and 99.8% negative agreement for N. gonorrhoeae. In limiting dilution analyses, we found that the Abbot assay was more sensitive than the Roche assay for both C. trachomatis and N. gonorrhoeae. In addition, there appeared to be an enhanced ability of the Abbott assay to detect dual infections, especially in the presence of large amounts of N. gonorrhoeae and small amounts of C. trachomatis organisms. In summary, we conclude that the Abbott RealTime CT/NG assay is an accurate and automated new addition to the available testing options for C. trachomatis and N. gonorrhoeae.

Aetiological agents of urethritis in symptomatic South African men attending a family practice

The objective was to determine the occurrence of four urethral pathogens in urine specimens from symptomatic men using transcription mediated amplification (TMA) assay. Urethral swab and urine specimens from 300 men presenting to a family practitioner were Gram stained and tested for Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis and Mycoplasma genitalium using three TMA assays respectively. Except for T. vaginalis, the other recognized pathogens viz. N. gonorrhoeae, C. trachomatis and M. genitalium were detected in significantly larger numbers of patients with urethral discharge than in those with burning on micturition (BOM). The overall prevalences were 16.7% for N. gonorrhoeae, 12.3% C. trachomatis, 8.0% T. vaginalis and 17.3% M. genitalium. With regard to microscopic evidence of urethritis, significant associations were found for N. gonorrhoeae and C. trachomatis, but not for M. genitalium and T. vaginalis. This study demonstrated that in symptomatic men attending family practice, M. genitalium and T. vaginalis are also important aetiological agents of urethritis and hence treatment strategies be they syndromic management or laboratory directed should cover for these causative agents. The microscopic diagnosis of urethritis may not be important for treatment strategies. The current syndromic treatment guidelines for developing countries including South Africa need modification.

Nucleic Acid Amplification of the opa Gene for Detection of Neisseria gonorrhoeae: experience from a diagnostic laboratory

We report results of Neisseria gonorrhoeae nucleic acid amplification testing (NAAT) with the Abbott m2000 PCR at a tertiary laboratory 6 months after its introduction. Of 5,475 specimens tested, 45 samples (0.82%) tested positive for N. gonorrhoeae. Eight were not cultured, but seven tested positive with a porA pseudogene NAAT.

Comparison of Aptima Trichomonas vaginalis transcription-mediated amplification assay and BD affirm VPIII for detection of T. vaginalis in symptomatic women: performance parameters and epidemiological implications

Trichomonas vaginalis is an underestimated sexually transmitted infection (STI) associated with numerous clinical sequelae. The true prevalence and clinical impact of trichomoniasis are unknown, as current methods of detection exhibit poor sensitivity compared to molecular amplification methods. Limited data exist comparing the BD Affirm VPIII hybridization assay to the Gen-Probe Aptima T. vaginalis (ATV) transcription-mediated amplification (TMA) assay for detection of T. vaginalis. In this study, specimens from 766 patients were evaluated. Specimens were retrieved consecutively from patients with vaginal complaints and/or with histories suggestive of STI. Study inclusion was dependent upon the request for and collection of both a vaginal swab for Affirm and a specimen for Aptima Combo 2 by the health care provider during the same office visit. Affirm was performed using the specific collection swab and the transport provided for the test. The ATV assay was performed on remnant Aptima Combo 2 specimens. A second ATV TMA assay, utilizing an alternate T. vaginalis primer and probe set, was performed on all specimens positive by the initial TMA and/or the Affirm assay. Infected-patient status was defined as positive T. vaginalis test results by at least 2 assays. Overall, 5.1% of subjects were positive for T. vaginalis. T. vaginalis was most prevalent in women who were 36 to 45 (11.9%), 51 to 60 (7.7%), and 16 to 25 (4.2%) years of age. The ATV assay was statistically more sensitive than the Affirm assay (100% versus 63.4%, P < 0.0001), identifying 36.6% more positive patients.

Trichomonas vaginalis transcription-mediated amplification-based analyte-specific reagent and alternative target testing of primary clinical vaginal saline suspensions

Following wet mount analysis, 255 vaginal saline suspensions were aliquoted to lysis medium for transcription-mediated amplification (TMA)-based Trichomonas vaginalis analyte-specific reagent testing (ASR) (Gen-Probe, San Diego, CA). Specimens with visible T. vaginalis were then refrigerated, with additional aliquoting at later intervals. Twenty-four wet mount-positive specimens (9.4%) yielded a median luminescent value (x1000, relative light unit [RLU]) of 4736. In contrast, RLU ranged from 1 to 21 following ASR of 204 wet mount-negative specimens. Twenty-seven wet mount-negative specimens (10.5%) were positive by ASR and subsequently positive via T. vaginalis alternative target TMA (Gen-Probe). Discrepancies were additionally resolved by demonstration of T. vaginalis nucleic acid from a separate endocervical collection. T. vaginalis nucleic acid was detectable following prolonged storage, following minimal incubation in lysis medium, and from low-volume aliquots of sparsely populated specimens. T. vaginalis ASR adequately detects T. vaginalis from vaginal saline suspension aliquots, providing a simple specimen alternative for a highly sensitive laboratory diagnosis of trichomoniasis.

A German Chlamydia trachomatis screening program employing semi-automated real-time PCR: results and perspectives

BACKGROUND

Genital Chlamydia trachomatis infection is a worldwide public health burden. A screening program for C. trachomatis was therefore initiated by the public health insurers in Germany ("Gemeinsamer Bundesausschuss", GBA) in April 2008.

OBJECTIVES

To estimate C. trachomatis prevalence from screening 115,766 asymptomatic females and 20,033 female patients with unspecific abdominal pain.

STUDY DESIGN

Urine samples (pooled by five for the asymptomatic screening subjects) and cervical swabs were analyzed using semi-automated real-time PCR. Infection prevalence was determined separately in four categories of women, defined by health status (asymptomatic screening vs. non-screening with unspecified symptoms) and test material used. Comparative analyses were stratified by age and pregnancy status.

RESULTS

Experimental evaluation of the assay used revealed a detection limit of 379 genome copies/ml urine. For pooled urine samples, the positive predictive value was 100% whereas the negative predictive value equaled 98.1%. The observed infection prevalence was higher for cervical swabs than for urine samples. Prevalence estimates also differed significantly between pregnant and non-pregnant adolescents (< or = 20 years), irrespective of the test material used (10.2% vs. 7.3% for cervical swabs, 10.9% vs. 6.1% for pooled urine samples).

CONCLUSIONS

Our retrospective study, based upon a very large number of females from all parts of Germany, revealed a high infection prevalence in adolescents, particularly in pregnant adolescents, thereby justifying the screening directive of the German GBA.

Survey of sexually transmitted disease laboratory methods in US Army laboratories

BACKGROUND

Sexually transmitted diseases, in particular Chlamydia trachomatis and Neisseria gonorrhoeae, are ranked as the top 2 most commonly notified disease in the US Army. Although surveillance programs are in place to capture event data, no routine STD surveillance program captures laboratory test information.

METHODS

To evaluate laboratory testing practices/methodologies in US Army laboratories in 2007, a questionnaire was distributed to all 38 US Army laboratories. The results of the survey were compared across Army installations to US civilian public health laboratories.

RESULTS

Of 38 survey recipients, 35 (92.1%) completed the survey. Overall, 78.6% of C. trachomatis and 77.2% of N. gonorrhoeae specimens were tested by nucleic acid amplification tests. In addition, 48.6% used culture as a method of N. gonorrhoeae testing. Testing for genital herpes, trichomonas, bacterial vaginosis, syphilis, human papillomavirus, and/or premalignant/malignant cervical cells was performed by 33 of the 35 laboratories.

CONCLUSIONS

A high proportion of US Army laboratories are using NAAT technology for C. trachomatis and N. gonorrhoeae testing. A more comprehensive questionnaire may be needed to accurately describe the type and volume of other STD tests. Despite the difference in survey data acquisition between the US civilian public health laboratory survey and the US Army laboratory survey, broad comparisons such as test types were able to be made. Future surveys should be extended to other US military services and should include both civilian and military laboratories.

Isothermal DNA amplification in vitro: the helicase-dependent amplification system

Since the development of polymerase chain reaction, amplification of nucleic acids has emerged as an elemental tool for molecular biology, genomics, and biotechnology. Amplification methods often use temperature cycling to exponentially amplify nucleic acids; however, isothermal amplification methods have also been developed, which do not require heating the double-stranded nucleic acid to dissociate the synthesized products from templates. Among the several methods used for isothermal DNA amplification, the helicase-dependent amplification (HDA) is discussed in this review with an emphasis on the reconstituted DNA replication system. Since DNA helicase can unwind the double-stranded DNA without the need for heating, the HDA system provides a very useful tool to amplify DNA in vitro under isothermal conditions with a simplified reaction scheme. This review describes components and detailed aspects of current HDA systems using Escherichia coli UvrD helicase and T7 bacteriophage gp4 helicase with consideration of the processivity and efficiency of DNA amplification.

Process Evaluation of a Fully Automated Molecular Diagnostics System

Molecular diagnostics presents challenges to clinical laboratories that are under pressure to consolidate and automate. There is a need to evaluate molecular automation for process efficiency and suitability for high-throughput environments in core laboratories.

A fully automated molecular instrument platform (the BD Viper System with XTR Technology in extracted mode [BD Viper System with XTR]), was evaluated for automation efficiency, labor requirements, and system robustness. System productivity was predicted using time and motion studies as well as process simulation.

Preanalytical steps required 15 min of skilled operator time. The BD Viper System with XTR fully automated DNA extraction, amplification, and analysis of 368 specimens (736 results for Chlamydia and Gonorrhea). Time and motion studies estimated that the total hands-on full time employee (FTE) burden was approximately 35 min per run, of which 41% was high complexity, 29% medium complexity and 29% relatively unskilled labor. A skilled operator can easily operate four instruments for 8.5 h and generate data on 2944 results (four runs on each instrument for a total of 1472 clinical specimens) for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) analysis. Based on mean time between intervention data, the BD Viper System with XTR was estimated to be capable of operating for more than 1000 runs without system malfunction.

We determined that fully automated molecular analysis of GC and CT is possible in a core laboratory facility with significant throughput and minimal impact on labor demand using a fully automated and robust molecular diagnostics platform (such as the BD Viper System with XTR).