Characteristics of the m2000 automated sample preparation and multiplex real-time PCR system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae

Performance of Sexually Transmitted Disease Laboratories for Chlamydia trachomatis Detection in Guangdong, China

BACKGROUND

Chlamydia trachomatis detection plays a crucial role in early diagnosis and treatment of C. trachomatis infection. In the current study, the capability of sexually transmitted disease (STD) laboratories to detect C. trachomatis was investigated in Guangdong, China.

METHODS

An external quality assessment panel, including 5 positive samples with different C. trachomatis loads and 2 negative samples was distributed to 654 participating laboratories in October 2019, and the test results were analyzed by Guangdong Central STD Laboratory. The use of various C. trachomatis detection methods in Guangdong from 2015 to 2019 was also retrospectively investigated.

RESULTS

Of the 654 participating STD laboratories, 559 (85.47%) used immune chromatographic-rapid diagnostic tests (IC-RDTs) to detect C. trachomatis in 2019, and 95 (14.53%) used nucleic acid amplification tests (NAATs). The rate of NAATs use increased approximately 4-fold from 2015 to 2019. The sensitivity of IC-RDTs decreased markedly from 97.32% to 30.89% with decreasing C. trachomatis load, whereas that of NAATs was 97.62% to 100% in all positive samples. With respect to negative samples the specificity of IC-RDTs was 97.13% to 97.30% and that of NAATs was 98.95% to 100%. Laboratories using IC-RDTs were less likely to detect C. trachomatis than those using NAATs in samples with C. trachomatis loads of 20000 copies/mL or less (P < 0.0001). Further analysis indicated no significant difference (P > 0.05) in detection rate among the 4 IC-RDT assays commonly used by the participating laboratories.

CONCLUSIONS

Immune chromatographic-rapid diagnostic tests are commonly used for C. trachomatis detection by many laboratories in Guangdong, but their low sensitivity may lead to missed diagnoses. Nucleic acid amplification tests exhibit high sensitivity and specificity and should be recommended for C. trachomatis detection in STD laboratories.

Update on the Diagnosis of Sexually Transmitted Infections

Sexually transmitted infections (STIs) are one of the most frequent and universal Public Health problems. Health professionals should be aware of the possibility of STIs due to their high morbidity and the presence of sequelae. The delay in the diagnosis is one of the factors that justifies the difficulty to infections control. Diagnostic tests allow the introduction of aetiological treatment and also lead to treating symptomatic and asymptomatic patients more effectively, as well as to interrupt the epidemiological transmission chain without delay. In this review we have made an update of the main existing diagnostic methods for the more important STIs.

Sensitivity and Specificity of Empiric Treatment for Sexually Transmitted Infections in a Pediatric Emergency Department

OBJECTIVE

To determine test characteristics of provider judgment for empiric antibiotic provision to patients undergoing testing for a sexually transmitted infection.

STUDY DESIGN

We conducted a retrospective cross-sectional electronic health record review of all patients aged 13-19 years who had Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) testing sent from an urban, academic pediatric emergency department in 2012. We abstracted data, including patient demographics, chief complaint, sexually transmitted infection test results, and treatment. We calculated test characteristics comparing clinician judgment for presumptive treatment for a sexually transmitted infection with the reference standard of the actual results of testing for a sexually transmitted infection.

RESULTS

Of 1223 patient visits meeting inclusion criteria, 284 (23.2%) had a positive GC and/or CT test result. Empiric treatment was provided in 615 encounters (50.3%). Provider judgment for presumptive treatment had an overall sensitivity of 67.6% (95% CI, 61.8-73.0) and a specificity of 55% (95% CI, 51.7-58.2) for accurate GC and/or CT detection.

CONCLUSIONS

Many adolescents tested for GC and CT receive empiric treatment at the initial emergency department visit. Provider judgment may lack sufficient sensitivity and specificity for identifying infected patients, resulting in the potential for undertreatment of true disease, overtreatment of uninfected patients, or both.

Detection of Chlamydia trachomatis and Neisseria gonorrhoeae based on cross-priming amplification

Rapid, sensitive and specific isothermal nucleic acid amplification methods of Chlamydia trachomatis (C. trachomatis) and Neisseria gonorrhoeae (N. gonorrhoeae) have been developed based on cross-priming amplification (CPA). The amplicon of CPA can be detected by a disposable amplicon cross-contamination proof device. The whole assay takes 1-1·5 h from amplification to read out. Ten fold serial dilutions of quantified plasmids were used to test the CPA assay sensitivities, with the detection limits of 45 copies per reaction and 65 copies per reaction for C. trachomatis and N. gonorrhoeae respectively. The specificities of CPA assays for C. trachomatis and N. gonorrhoeae were tested by using total DNA extracted from nine other bacterial strains, and no cross-reactivity was detected. Eighty clinical cervical or vaginal swab specimens were tested by both CPA and real-time polymerase chain reaction (PCR) with the consistencies of 98·75% (79/80) and 97·5% (78/80) for C. trachomatis and N. gonorrhoeae respectively. Using real-time PCR as a reference standard, the clinical sensitivity (positive) and specificity (negative) of CPA was found to be 98·15% (53/54) and 100% (26/26) for C. trachomatis, and 93·75% (30/32) and 100% (48/48) for N. gonorrhoeae. Eight swab specimens tested positive for both C. trachomatis and N. gonorrhoeae simultaneously by real-time PCR and CPA assay. This study demonstrated that CPA is an affordable and accessible assay for C. trachomatis and N. gonorrhoeae detection, with high sensitivity and specificity.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid and specific detection of the sexually transmitted pathogens Chlamydia trachomatis (C. trachomatis) and Neisseria gonorrhoeae (N. gonorrhoeae) would enable early treatment and management of their spread. Here, for the first time, a user friendly DNA isothermal amplification method named cross-priming amplification (CPA), was used to test C. trachomatis and N. gonorrhoeae with high sensitivity and specificity. The results indicate that CPA has great potential for improving C. trachomatis and N. gonorrhoeae diagnostics which could be particularly advantageous in resource-limited areas.

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.

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 Abbott RealTime CT/NG assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in cervical swabs from female sex workers in China

Background

To evaluate the performance of the Abbott RealTime CT/NG assay for detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) among female sex workers (FSWs) in China.

Methods

Cervical swabs from 997 participants were blindly detected by the Abbott RealTime CT/NG assay on the automated m2000 molecular platform and Roche Cobas Amplicor CT/NG assay. Discrepant analysis were confirmed by the Qiagen care CT PCR assay. The sample was defined as candidate nvCT-positive if it was CT positive in the Abbott m2000 assay, but CT negative in the other two assays.

Results

25 specimens that were discordant for CT and 26 specimens that were discordant for NG between the two assays were resolved by Qiagen care CT & NG PCR assays. The sensitivity and specificity, respectively, for Abbott m2000 assay were 92.59% and 100% for CT and 95.45% and 99.90% for NG. The positive predictive value (PPV) and negative predictive value (NPV) of Abbott m2000 assay were100% and 98.52% for CT and 95.5% and 99.90% for NG, respectively. No candidate new-variant CT(nvCT)specimens were identified.

Conclusion

Abbott RealTime CT/NG assay were more specify for CT and NG detection, however, its sensitivity for CT and NG were a little bit lower than Roche Cobas Amplicor CT/NG assay. Abbott RealTime CT/NG assay had higher PPV for NG detection than Roche Cobas Amplicor CT/NG assay; it would be more suitable for screening for population with low-prevalence NG. There is currently no evidence that nvCT is present in FSWs in China.

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.

Real-time PCR as a diagnostic tool for bacterial diseases

In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.

Comparative evaluation of the Abbott HIV-1 RealTime™ assay with the Standard Roche COBAS® Amplicor™ HIV-1 Monitor® Test, v1.5 for determining HIV-1 RNA levels in plasma specimens from Pune, India

The implementation of cost effective HIV-1 viral load assays in resource-limited settings have been an impediment for monitoring HIV-1 therapy. A study involving the comparative analytical performance of two HIV-1 viral load assays - Standard Roche COBAS(®) Amplicor™ HIV-1 Monitor(®) Test, version 1.5 (Roche Diagnostics, Basel, Switzerland) and Abbott HIV-1 RealTime™ assay (Abbott Molecular, Wiesbaden, Germany) was performed using 125 specimens in Pune, India. A strong correlation was observed between the manual endpoint reverse transcriptase polymerase chain reaction assay and the recent real time polymerase chain reaction assay (r=0.989, p value<0.0001) and agreement was 94.4%. Results of the study indicate a higher sensitivity of the Abbott HIV-1 RealTime™ assay for HIV-1 Virology Quality Assurance copy controls as compared to the Standard Roche COBAS(®) Amplicor™ HIV-1 Monitor(®) Test, version 1.5. Furthermore, features of the Abbott m2000rt RealTime™ PCR assay platform such as higher analytical sensitivity, automated/manual extraction platforms for high/low sample throughputs and ability to quantify a variety of infectious agents (Hepatitis B virus, Hepatitis C virus, Human Papillomavirus and Neisseria gonorrhoeae/Chlamydia trachomatis) justify its suitability in resource-limited Indian settings. Besides, the study also highlights utility of the precise Virology Quality Assurance validation template in performance evaluation of various quantitative viral load assays.

[Diagnosis and treatment of Chlamydia trachomatis infections]

Nucleic acid amplification tests are now considered the method of choice to detect Chlamydia trachomatis. These assays have highest sensitivity and also high specificity, comparable to culture. First-void urine is the preferred specimen for urogenital infections of males, whereas vaginal and cervical swabs are at least as effective for testing female lower genital tract infections. Chlamydia point-of-care tests may produce results rapidly without special equipment but lack diagnostic accuracy and thus are unsuitable for routine use. Serology is not useful for detection of acute infections, but may help to identify persistent infections with Chlamydia no longer detectable in swabs or urine specimens. Various guidelines recommend doxycycline and azithromycin for treatment of uncomplicated Chlamydia infection. Alternatively erythromycin, ofloxacin and levofloxacin can be used. Persistent infections usually require treatment for longer periods or by using combinations of different antibiotics.

Chlamydia trachomatis infection in fertile and subfertile women in Rwanda: prevalence and diagnostic significance of IgG and IgA antibodies testing

BACKGROUND

In many developing countries, little is known about the prevalence of genital Chlamydia trachomatis infections and complications, such as infertility, thus preventing any policy from being formulated regarding screening for C. trachomatis of patients at risk for infertility. The objective of the present study was to determine the prevalence of C. trachomatis and evaluate the diagnostic utility of serological markers namely anti-C. trachomatis IgG and IgA antibodies in women attending an infertility clinic.

METHODS

Serum and vaginal swab specimens of 303 women presenting with infertility to the infertility clinic of the Kigali University Teaching Hospital and 312 fertile controls who recently delivered were investigated. Two commercial species-specific ELISA were used to determine serum IgG and IgA antibodies to C. trachomatis and vaginal swabs specimens were tested by PCR. Hysterosalpingography (HSG) was performed in subfertile women.

RESULTS

The PCR prevalence of C. trachomatis infection was relatively low and did not differ significantly among subfertile and fertile women (3.3 versus 3.8%). Similarly, no significant differences in overall prevalence rates of C. trachomatis IgG and IgA among both groups were observed. The only factor associated with C. trachomatis infection in our study population was age <25 years. The seroprevalence of IgG in both assays (86.4% for ANILabsystems and 90.9% for Vircell) was significantly higher in the group of PCR C. trachomatis-positive women compared with that of PCR-negative women. Evidence of tubal pathology identified by HSG was found in 185 patients in the subfertile group (67.8%). All the serological markers measured in this study had very low sensitivities and negative predictive values in predicting tubal pathology. The specificities for ANILabsystems IgG, Vircell IgG, Anilabsystem IgA and positive C. trachomatis DNA to predict tubal pathology were 84, 86, 95 and 98%, respectively, whereas their respective positive predictive values were 73, 76, 81 and 80%.

CONCLUSIONS

The prevalence of C. trachomatis in our study population in Rwanda appears to be low and women aged <25 years are more likely to have genital infection with C. trachomatis. Since serological testing for Chlamydia shows an excellent negative predictive value for lower genital tract infection, specific peptide-based serological assays may be of use for screening in low prevalence settings. Our data suggest that C. trachomatis is not the primary pathogen responsible for tubal pathology in Rwandan women.

A novel RealTime HIV-1 Qualitative assay for the detection of HIV-1 nucleic acids in dried blood spots and plasma

Abbott RealTime HIV-1 Qualitative is an in vitro real-time PCR assay for detecting HIV-1 nucleic acids in human plasma and dried blood spots (DBS). The assay was designed to be used in diagnosis of HIV-1 infections in pediatric and adult patients, with an emphasis on the applicability in resource-limited settings. Use of DBS facilitates specimen collection from remote areas and transportation to testing laboratories. Small sample input requirement facilitates testing of specimens with limited collection volume. The Abbott RealTime HIV-1 Qualitative assay is capable of detecting HIV-1 group M subtypes A-H, group O and group N samples. HIV-1 virus concentrations detected with 95% probability were 80 copies/mL of plasma using the plasma protocol, and 2469 copies/mL of whole blood using the DBS protocol. The assay detected HIV-1 infection in 13 seroconversion panels an average 10.5 days earlier than an HIV-1 antibody test and 4.9 days earlier than a p24 antigen test. For specimens collected from 6 weeks to 18 months old infants born to HIV-1 positive mothers, assay results using both the DBS and plasma protocols agreed well with the Roche Amplicor HIV-1 DNA Test version 1.5 (95.5% agreement for DBS and 97.8% agreement for plasma).

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.

[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.

Epidemiological features and determinants for Chlamydia trachomatis infection among women in Catalonia, Spain

We determined the prevalence of Chlamydia trachomatis (CT) infection and risk factors for its acquisition by women aged less than 35 years who were attending sexual health centres in the province of Barcelona in 2007. A convenience sample of 397 adolescents and young adult women aged between 16 and 35 years, stratified by age and recruitment site, were tested using realtime polymerase chain reaction by CT DNA. A standardized questionnaire was used to collect epidemiological and behavioural data on the participants, which were analysed in a multivariate logistic regression model. The overall prevalence of CT was 4%, significantly higher in those under 25 years of age (5.8% versus 1.6% over 25). The independent risk factors for CT infection were: foreign origin (odds ratio [OR] 4.7; confidence interval [CI] 1.02-21.8), having had a sexual partner in the last three months (OR 4.59; CI 1.16-18.08) and tobacco use the last 12 months (OR 6.38; CI 1.16-34.93). In conclusion, this is the first study performed in Catalonia showing a high prevalence of CT in young women, consistent with trends in the rest of Europe. Systematic monitoring of CT infection in sentinel populations such as this will inform future targeted screening programmes in our setting.

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.

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.

Rapid homogeneous PCR assay for the detection of Chlamydia trachomatis in urine samples

Chlamydia trachomatis infection is the most common bacterial sexually transmitted disease and a major public health problem worldwide. Fast and sensitive point-of-care diagnostics including non-invasive sample collection would be of value for the prevention of C. trachomatis transmission. The aim of this study was to develop a fast, reliable, non-invasive and easy-to-use homogenous PCR assay for the detection of C. trachomatis. Bacteria were concentrated from urine by a simple and fast centrifugation-based urine pretreatment method. Novel automated GenomEra technology was utilized for the rapid closed-tube PCR including time-resolved fluorometric detection of the target using lanthanide chelate labeled probes. We have developed a rapid C. trachomatis assay which provides qualitative results in 1 h with diagnostic sensitivity and specificity of 98.7% and 97.3%, respectively. The novel assay can be performed with minimal laboratory expertise and without sophisticated DNA-extraction devices and has performance comparable to current gold standard assays.

Immiscible phase nucleic acid purification eliminates PCR inhibitors with a single pass of paramagnetic particles through a hydrophobic liquid

Extraction and purification of nucleic acids from complex biological samples for PCR are critical steps because inhibitors must be removed that can affect reaction efficiency and the accuracy of results. This preanalytical processing generally involves capturing nucleic acids on microparticles that are then washed with a series of buffers to desorb and dilute out interfering substances. We have developed a novel purification method that replaces multiple wash steps with a single pass of paramagnetic particles (PMPs) though an immiscible hydrophobic liquid. Only two aqueous solutions are required: a lysis buffer, in which nucleic acids are captured on PMPs, and an elution buffer, in which they are released for amplification. The PMPs containing the nucleic acids are magnetically transported through a channel containing liquid wax that connects the lysis chamber to the elution chamber in a specially designed cartridge. Transporting PMPs through the immiscible phase yielded DNA and RNA as pure as that obtained after extensive wash steps required by comparable purification methods. Our immiscible-phase process has been applied to targets in whole blood, plasma, and urine and will enable the development of faster and simpler purification systems.

Taqman real-time PCR detects Avipoxvirus DNA in blood of Hawai'i 'amakihi (Hemignathus virens)

Background

Avipoxvirus sp. is a significant threat to endemic bird populations on several groups of islands worldwide, including Hawaìi, the Galapagos Islands, and the Canary Islands. Accurate identification and genotyping of Avipoxvirus is critical to the study of this disease and how it interacts with other pathogens, but currently available methods rely on invasive sampling of pox-like lesions and may be especially harmful in smaller birds.

Methodology/Principal Findings

Here, we present a nested TaqMan Real-Time PCR for the detection of the Avipoxvirus 4b core protein gene in archived blood samples from Hawaiian birds. The method was successful in amplifying Avipoxvirus DNA from packed blood cells of one of seven Hawaiian honeycreepers with confirmed Avipoxvirus infections and 13 of 28 Hawaìi `amakihi (Hemignathus virens) with suspected Avipoxvirus infections based on the presence of pox-like lesions. Mixed genotype infections have not previously been documented in Hawaìi but were observed in two individuals in this study.

Conclusions/Significance

We anticipate that this method will be applicable to other closely related strains of Avipoxvirus and will become an important and useful tool in global studies of the epidemiology of Avipoxvirus.

Rapid and specific detection of amantadine-resistant influenza A viruses with a Ser31Asn mutation by the cycling probe method

Amantadine is one of the antiviral agents used to treat influenza A virus infections, but resistant strains have widely emerged worldwide. In the present study, we developed a novel method to detect amantadine-resistant strains harboring the Ser31Asn mutation in the M2 gene based on the cycling probe method and real-time PCR. We also studied the rate of amantadine resistance in the 2007-2008 influenza season in Japan. Two different primer and cycling probe sets were designed for A/H1N1 and A/H3N2 each to detect a single nucleotide polymorphism corresponding to Ser/Asn at residue 31 of the M2 protein. By using nasopharyngeal swabs from patients with influenza-like and other respiratory illnesses and virus isolates, the specificity and the sensitivity of the cycling probe method were evaluated. High frequencies of amantadine resistance were detected among the A/H1N1 (411/663, 62%) and A/H3N2 (56/56, 100%) virus isolates collected from six prefectures in Japan in the 2007-2008 influenza season. We confirmed that the cycling probe method is suitable for the screening of both nasopharyngeal swabs and influenza virus isolates for amantadine-resistant strains and showed that the incidence of amantadine resistance among both A/H1N1 and A/H3N2 viruses remained high in Japan during the 2007-2008 season.

Chlamydia trachomatis today: treatment, detection, immunogenetics and the need for a greater global understanding of chlamydial disease pathogenesis

Chlamydia trachomatis is an important human pathogen causing a myriad of severe and debilitating diseases. While antibiotics have been a mainstay of treatment, there is increasing evidence for potential drug resistance, reinfection and persistent infections that require a reevaluation of treatment strategies. A critical need to address these issues will be a rapid, sensitive and cost-effective diagnostic that can be used for global screening, treatment and test-of-cure of infected individuals instead of empirical therapy that not only drives drug resistance but is not costeffective. This type of diagnostic would allow clinicians and researchers to evaluate the true incidence and prevalence of chlamydial infections in both developed and developing countries. There are extremely limited data on chlamydial sexually transmitted diseases (STDs) in many developing countries, including those in Central and South America. In addition, advancing our understanding of chlamydial disease pathogenesis will require an evaluation of host genetic susceptibility to infection and sequelae. We provide preliminary data on rates of chlamydial STDs and host genetic factors that predispose to infection among adolescent pregnant and nonpregnant commercial sex worker populations residing in Quito, Ecuador.

Evaluation of the Abbott m2000 RealTime human immunodeficiency virus type 1 (HIV-1) assay for HIV load monitoring in South Africa compared to the Roche Cobas AmpliPrep-Cobas Amplicor, Roche Cobas AmpliPrep-Cobas TaqMan HIV-1, and BioMerieux NucliSENS EasyQ HIV-1 assays

The implementation of antiretroviral therapy demands the need for increased access to viral load (VL) monitoring. Newer real-time VL testing technologies are faster and have larger dynamic ranges and fully automated extraction to benefit higher throughputs in resource-poor environments. The Abbott RealTime human immunodeficiency virus type 1 (HIV-1) assay was evaluated as a new option for testing for HIV-1 subtype C in South Africa, and its performance was compared to the performance of existing assays (the Cobas AmpliPrep-Cobas TaqMan HIV-1, version 1, assay; the AmpliPrep-Cobas Monitor standard HIV-1 assay; and the NucliSENS EasyQ-EasyMag HIV-1 assay) in a high-throughput laboratory. The total precision of the RealTime HIV-1 assay was acceptable over all viral load ranges. This assay compared most favorably with the Cobas AmpliPrep-Cobas TaqMan HIV-1 assay (R(2) = 0.904), with a low standard deviation of difference being detected (0.323 copies/ml). The bias against comparator assays ranged from -0.001 copies/ml to -0.228 copies/ml. Variability in the reporting of VLs for a 20-member subtype panel compared to the variability of other assays was noted with subtypes G and CRF02-AG. The RealTime HIV-1 assay can test 93 samples per day with minimal manual preparation, less staff, and the minimization of contamination through automation. This assay is suitable for HIV-1 subtype C VL quantification in South Africa.

Comparison of Gen-probe transcription-mediated amplification, Abbott PCR, and Roche PCR assays for detection of wild-type and mutant plasmid strains of Chlamydia trachomatis in Sweden

The clinical performance of two nucleic acid amplification assays targeting the cryptic plasmid and two assays targeting rRNA molecules in Chlamydia trachomatis was examined. First-catch urine samples from Malmoe, Sweden, were tested for C. trachomatis with the Abbott real-time PCR assay m2000 and an in-house PCR for the new variant strain of C. trachomatis with a deletion in the cryptic plasmid. Aliquots of the urine samples were sent to Aarhus, Denmark, and further examined with the Roche COBAS Amplicor CT (RCA) PCR, the Gen-Probe Aptima Combo 2 assay (AC2) targeting the C. trachomatis 23S rRNA, and the Aptima C. trachomatis assay (ACT) targeting the 16S rRNA molecule. A positive prevalence of 9% (163/1,808 urine samples examined) was detected according to the combined reference standard. The clinical sensitivity and specificity of the four assays were as follows: for ACT, 100% (163/163) and 99.9% (1,643/1,645), respectively; for AC2, 100% (163/163) and 99.6% (1,640/1,645); for m2000, 68.7% (112/163) and 99.9% (1,644/1,645); for RCA, 63.8% (104/163) and 99.9% (1,643/1,645). The two Gen-Probe assays detected all mutant strains characterized by the in-house PCR as having the deletion in the cryptic plasmid, whereas the Roche and the Abbott PCRs targeting the plasmid were both unable to detect the plasmid mutant. The difference in clinical sensitivity between the plasmid PCR assays m2000 and RCA, on the one hand, and the rRNA assays AC2 and ACT, on the other, could be attributed almost exclusively to the presence of the plasmid mutant in about one-quarter of the Chlamydia-positive samples examined.

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

A total of 500 first-void urine specimens were tested for the presence of Chlamydia trachomatis and Neisseria gonorrhoeae nucleic acids using ProbeTec ET reagents on a Viper platform (BD Diagnostics, Mississauga, Ontario, Canada), Aptima Combo 2 reagents on a Tigris platform (Gen-Probe, Inc., San Diego, CA), and Abbott RealTime CT/NG reagents on an m2000 platform (Abbott Molecular Diagnostics, Des Plaines, IL). The performance of the three assays for detection of N. gonorrhoeae was comparable, but detection of C. trachomatis by the three assays showed more variation. All three platforms were suitable for the detection of C. trachomatis and N. gonorrhoeae, but additional factors, such as maximum daily specimen throughput, are important in evaluating automated systems for C. trachomatis and N. gonorrhoeae detection in high-volume laboratories.