Commercial Polymerase Chain Reaction Assay Research Articles

Assessment of Commercial Real-Time PCR Assays for Detection of Malaria Infection in a Non-Endemic Setting.

Malaria control and elimination require prompt diagnosis and accurate treatment. Conventional methods such as rapid diagnostic tests (RDTs) and microscopy lack the characteristics to detect low parasitemias, commonly found in asymptomatic parasitemias and/or submicroscopic malaria carriers. On the contrary, molecular methods have higher sensitivity and specificity. This study evaluated the performance of two commercial real-time polymerase chain reaction (PCR) assays, RealStar® Malaria PCR (RealStar-genus) and RealStar Malaria Screen&Type PCR (RealStar-species), compared with the reference Nested Multiplex Malaria PCR, for the detection of the main five Plasmodium species affecting humans. A total of 121 samples were evaluated. Values of sensitivity (98.9% and 97.8%) and specificity (100% and 96.7%) of the RealStar-genus and the RealStar-species assays, respectively, were very good. The limit of detection (LoD) for the RealStar-genus assay showed a mean value of 0.28 parasites/µL with Plasmodium falciparum samples; while, the LoD of the RealStar-species assay ranged from 0.09 parasites/µL for P. vivax to two parasites/µL for P. ovale. The time to complete a diagnosis was established in 4 hours. Our findings showed a very good concordance of both assays compared with the reference method, with a very good analytical sensitivity. RealStar-species assay was able to correctly characterize double and triple infections. Therefore, these RealStar assays have shown to be useful tools in malaria diagnosis in non-endemic countries and even endemic countries, and for malaria control in general, detecting low parasitemias with sensitivity similar to the most sensitive methods as nested PCR, but with lower time to get the results.

Multi-assay investigation of viral etiology in pediatric central nervous system infections.

In an attempt to identify a wide spectrum of viral infections, cerebrospinal fluid (CSF) specimens were collected from pediatric cases with the preliminary diagnosis of viral encephalitis/meningoencephalitis in two reference hospitals, from October 2011 to December 2015. A combination of nucleic acid-based assays, including in house generic polymerase chain reaction (PCR) assays for enteroviruses, flaviviruses and phleboviruses, a commercial real-time PCR assay for herpesviruses and a commercial real time multiplex PCR, enabling detection of frequently-observed viral, bacterial and fungal agents were employed for screening. The microbial agent could be characterized in 10 (10%) of the 100 specimens. Viral etiology could be demonstrated in 7 (70%) specimens, which comprises Human Herpesvirus 6 (4/7), Herpes Simplex virus type1 (2/7) and Enteroviruses (1/7). In 3 specimens (30%), Streptococcus pneumoniae, Listeria monocytogenes and Staphylococcus aureus were detected via the multiplex PCR, which were also isolated in bacteriological media. All specimens with detectable viral nucleic acids, as well as unreactive specimens via nucleic acid testing remained negative in bacteriological cultures. Herpes and enteroviruses were identified as the primary causative agents of central nervous system infections in children. Enterovirus testing must be included in the diagnostic work-up of relevant cases.

Diagnosing Pneumocystis jirovecii pneumonia: A review of current methods and novel approaches.

Pneumocystis jirovecii can cause life-threatening pneumonia in immunocompromised patients. Traditional diagnostic testing has relied on staining and direct visualization of the life-forms in bronchoalveolar lavage fluid. This method has proven insensitive, and invasive procedures may be needed to obtain adequate samples. Molecular methods of detection such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and antibody-antigen assays have been developed in an effort to solve these problems. These techniques are very sensitive and have the potential to detect Pneumocystis life-forms in noninvasive samples such as sputum, oral washes, nasopharyngeal aspirates, and serum. This review evaluates 100 studies that compare use of various diagnostic tests for Pneumocystis jirovecii pneumonia (PCP) in patient samples. Novel diagnostic methods have been widely used in the research setting but have faced barriers to clinical implementation including: interpretation of low fungal burdens, standardization of techniques, integration into resource-poor settings, poor understanding of the impact of host factors, geographic variations in the organism, heterogeneity of studies, and limited clinician recognition of PCP. Addressing these barriers will require identification of phenotypes that progress to PCP and diagnostic cut-offs for colonization, generation of life-form specific markers, comparison of commercial PCR assays, investigation of cost-effective point of care options, evaluation of host factors such as HIV status that may impact diagnosis, and identification of markers of genetic diversity that may be useful in diagnostic panels. Performing high-quality studies and educating physicians will be crucial to improve the rates of diagnosis of PCP and ultimately to improve patient outcomes.

Detection and identification of dermatophyte fungi in clinical samples using a commercial multiplex tandem PCR assay

We evaluated the performance of a commercial multiplex tandem polymerase chain reaction (PCR) for detection of dermatophytes and other fungi in skin and nail specimens by (1) testing a range of fungal and bacterial reference cultures, (2) retrospectively testing a set of skin and nail specimens with known microscopy and culture results, and (3) prospectively testing skin and nail specimens in parallel to microscopy and culture. The AusDiagnostics Dermatophytes and Other Fungi assay accurately detected and identified a range of common dermatophytes to species, species complex or genus level, as well as Candida, Aspergillus and Scopulariopsis spp. It was unable to detect uncommon dermatophytes such as Nannizzia fulva (previously Microsporum fulvum), and Paraphyton cookei (previously Microsporum cookei). PCR identified a dermatophyte in 25.9% of prospective specimens which were culture negative. Sensitivity, specificity, positive predictive value, and negative predictive value were highest where microscopy and PCR results were combined, versus microscopy and culture combined, which highlights the significant contribution of microscopy in the diagnostic pathway. This assay has the potential to reduce the workload and results turnaround time associated with culturing and identification of dermatophytes, although microscopy remains important.

Evaluation of Commercially Available Real-Time Polymerase Chain Reaction Assays for the Diagnosis of Invasive Aspergillosis in Patients with Haematological Malignancies.

Early diagnosis of invasive aspergillosis (IA) is a challenge. Non-specific clinical and radiologic findings, as well as difficulties in conventional diagnostic method application, may delay correct diagnosis. Nowadays, nucleic acid-based assays have reduced the need for conventional antigen detection and culture-based methods and provided new opportunities for patient care. Aspergillus PCR is now included in the latest European Cancer Research and Treatment Organization/Mycosis Study Group definition updates. We evaluated the performance of commercial real-time polymerase chain reaction (PCR) MycAssay Aspergillus PCR and Artus Aspergillus RG PCR assays and compared the results with galactomannan enzyme immunoassay. During 41 febrile neutropenic episodes, 168 serum samples were collected from 32 patients with haematological malignancies. IA diagnosis was established according to the revised guidelines of the European Organization for Research and Treatment of Cancer/Mycoses Study Group. Twenty-one probable episodes were identified. There were no proven IA cases in the study. In 20 episodes, patients did not fulfil the established criteria for the IA diagnosis. Artus Aspergillus RG PCR assay had a sensitivity of 47.6% and specificity of 100%, while those of MycAssay Aspergillus PCR were 61.9% and 100%, respectively. Two different PCR assays were used in this study. Although there are many studies that evaluated MycAssay Aspergillus PCR, data regarding Artus Aspergillus RG PCR assay are scarce. We found moderate sensitivity and high specificity in the diagnosis of IA in patients with haematological malignancy in both PCR methods. Our results demonstrated that commercial PCR assays can be applied for the early diagnosis and pre-emptive treatment of IA.

Incidence of matrix genes mutations affecting PCR tests among influenza H3N2 clades circulating during the 2014/15 season

Influenza circulating during the 2014/15 season was associated with significant drift and the emergence of new H3N2 subgroups. It was also known that mutations were accumulating in the WHO-recommended amplification region of the M1 gene, affecting the performance of many commercial polymerase chain reaction assays. However, the prevalence of M1 target mutations was unknown. To investigate this, isolates from the GISAID database from Australia (n=100), Europe (n=473), and the USA (n=1175) were analyzed. The predominate clade was 3C.2a (75%), with a higher representation among USA isolates (81%). The M1 target demonstrated four primary sequence patterns, designated A–D. Pattern D was most often observed (84%). Some clades correlated with M1 target patterns, as seen between subclades 3C.2a and 3C.3a and patterns D and C, respectively. 3C.3 isolates were more diverse, with three patterns represented. Among the 3C.3b isolates, pattern B predominated in non-USA viruses, while pattern D predominated among USA isolates.

Comparison of a new commercial real-time PCR assay (RealCycler PJIR kit, Progenie Molecular) to an in-house real-time PCR assay for the diagnosis of Pneumocystis jirovecii infections

The atypical fungus Pneumocystis jirovecii ( P. jirovecii ) is the causative agent of a life threatening pneumonia [ Pneumocystis pneumonia (PCP)] in immunosuppressed patients. PCP diagnosis is essentially based on the detection of the fungus in pulmonary specimens using microscopic examination and polymerase chain reaction (PCR). For the past 20 years, the use of PCR assays has improved the sensitivity of P. jirovecii detection. The main objective of the present study was to compare the efficiency of the RealCycler PJIR kit (Progenie Molecular; pmPCR), to an in-house PCR assay (ihPCR), both assays targeting the mitochondrial large subunit ribosomal rRNA gene. Thirty-four patients were retrospectively enrolled in the study. Fourteen patients were initially diagnosed with PCP, 15 were considered to be pulmonary colonized by the fungus, and five were negative for P. jirovecii detection (negative control group). Archival DNA specimens (extracted from the patient's pulmonary specimens) were examined with ihPCR and pmPCR on the same day using the same real-time PCR instrument (Applied Biosystems 7500 Real-Time PCR system). The ihPCR assay was performed as described elsewhere by Meliani et al. and Totet et al. [1,2] . The pmPCR assay was performed according to the manufacturer's recommendations. Concordant results were obtained with the two PCR assays for all DNA specimens but one (33/34). Thus, the concordance rate between the two methods was evaluated at 97% (Cohen's kappa, 0.905). The discrepant result concerned one specimen from a colonized patient previously known to have a cycle threshold (Ct) value ≥ 35 using ihPCR. This specimen was confirmed to be positive with ihPCR and was negative with pmPCR. Taking into account Ct values for positive samples, the correlation factor between the two PCR methods has been evaluated at 0.97 ( R 2 = 0.9481). Taking into account the Cohen's kappa > 0.8, the RealCycler PJIR kit (Progenie Molecular) appears to be an efficient technique to detect P. jirovecii in patients with PCP and in patients colonized by P. jirovecii .

Similar proportions of stool specimens from hospitalized children with and without diarrhea test positive for Clostridium difficile.

Many laboratories use polymerase chain reaction (PCR)-based assays to detect the Clostridium difficile toxin B gene (tcdB) in stool. However, PCR testing experience in pediatric patients is limited. We compared the detection of C. difficile by PCR in hospitalized children with and without diarrhea. Stool samples from patients aged 1-18 years with diarrhea (symptomatic) and from patients without diarrhea (asymptomatic) were tested for C. difficile tcdB using a commercial PCR assay. Samples were cultured for C. difficile using standard techniques with tcdB PCR and cytotoxicity assays performed on C. difficile isolates. Demographic, clinical and laboratory data were abstracted. Categorical and continuous variables were compared between the 2 groups using Fisher Exact test and the Mann-Whitney test, respectively. Thirty-five of 188 (19%) stool samples from symptomatic patients and 18 of 74 (24%) samples from asymptomatic patients were positive by PCR (P=0.31). Among PCR-positive patients, symptomatic patients had a significantly higher proportion of subjects who received antimicrobials in the preceding 30 days (P=0.04) and a greater number of preceding antimicrobial days than did asymptomatic patients (P=0.02) but were comparable with respect to the other variables analyzed. C. difficile PCR assays are frequently positive in hospitalized children both with and without diarrhea. As we observed a high level of toxigenic C. difficile colonization in children, our findings suggest that a positive C. difficile PCR result in a child with diarrhea should be interpreted with caution.

Detection of methicillin-resistant Staphylococcus aureus using a gold nanoparticle-based colourimetric polymerase chain reaction assay

We report the use of gold nanoparticles (Au NPs) for direct colourimetric polymerase chain reaction (PCR) detection of methicillin-resistant Staphylococcus aureus (MRSA) in clinical specimens. The colourimetric assay comprised of 2 Au NP probes functionalized with Staphylococcus aureus 23S rRNA- and mecA-specific oligonucleotides. In this study, 72 clinical samples were tested, which included positive blood culture (n=23), urine (n=8), respiratory samples (n=23), as well as wound swabs, pus and body fluid (n=18). Results were recorded qualitatively by direct visual examination and quantitatively by UV–vis spectrophotometry. Using conventional bacterial culture as the gold standard, the sensitivity, specificity, positive predictive value and negative predictive value of this colourimetric assay were 97.14%, 91.89%, 91.89% and 97.14%, respectively, which were comparable to that of commercial real-time PCR assays with a lower cost per reaction. Our assay also showed good agreement with bacterial culture (κ=0.889). The overall detection limit was 500ng target amplicon, which was comparable to or better than other similar Au NP biosensors. Interestingly, our data revealed the possible relationship between Au NP probe-target hybridization site and assay performance, which might provide hints for design of the Au NP biosensors for nucleic acid detection. To conclude, our study was the first report on the use of Au NP colourimetric assay for direct detection of MRSA in various types of clinical specimens. Further evaluation of the assay is needed in large-scale trials which can also allow for some modifications to streamline the procedures for routine use.

Evaluation of a commercial real-time polymerase chain reaction assay for detection of environmental contamination with Clostridium difficile

Contaminated environmental surfaces are an important source for transmission of Clostridium difficile. However, there are no efficient and easy methods to assess contamination. The performance of a commercial real-time polymerase chain reaction (PCR) assay was evaluated for detection of environmental toxigenic C.difficile in comparison with anaerobic culture followed by toxin testing of isolates. For 66 sites sampled, PCR had a sensitivity of 17.39%, specificity 100%, positive predictive value 100% and negative predictive value 69.35%. Increasing the PCR cycle threshold (CT) value to 45 increased sensitivity to 52% without decreasing specificity. The commercial PCR assay is not sufficiently sensitive for environmental monitoring, but improved sensitivity might be possible through CT value modification.

Prevalence ofMycobacterium aviumsubsp.paratuberculosisFecal Shedding in Alpacas Presented to Veterinary Hospitals in the United States

The prevalence of Johne's disease in alpacas in the United States is unknown. The limits of polymerase chain reaction (PCR) detection of Mycobacterium avium subsp. paratuberculosis (MAP) in alpaca feces have not been determined. To evaluate the use of PCR for MAP detection in alpaca feces; and to estimate the prevalence of MAP fecal shedding in alpacas presented to veterinary teaching hospitals. Alpacas presenting to 4 US veterinary teaching hospitals from November 2009 to February 2011. Prospective study. Ten dilutions of a wild MAP strain were added to negative alpaca feces and processed for MAP detection by means of a commercial real-time PCR (RT-PCR) assay, and cultured on Herrold's Egg Yolk Medium (HEYM) and liquid broth. The limits of detection for each method were determined. Fecal samples from alpacas admitted to the veterinary teaching hospitals during the study period were evaluated for MAP via PCR and HEYM. The lowest MAP dilution detectable via PCR was 243 MAP colony-forming units (CFU)/g of feces, at which concentration MAP growth was detectable on HEYM. Ten (6%; 95% confidence interval: 3-9%) of the 180 fecal samples collected were positive on PCR. Polymerase chain reaction can provide an accurate and rapid detection of MAP fecal shedding in alpacas; and the prevalence of MAP fecal shedding in hospitalized alpacas in 4 US veterinary teaching hospitals was 6%.

QUANTITATION OF HEPATITIS B VIRUS DNA IN PLASMA USING A SENSITIVE COST-EFFECTIVE “IN-HOUSE” REAL-TIME PCR ASSAY

Background: Sensitive nucleic acid testing for the detection and accurate quantitation of hepatitis B virus (HBV) is necessary to reduce transmission through blood and blood products and for monitoring patients on antiviral therapy. The aim of this study is to standardize an “in-house” real-time HBV polymerase chain reaction (PCR) for accurate quantitation and screening of HBV. Materials and Methods: The “in-house” real-time assay was compared with a commercial assay using 30 chronically infected individuals and 70 blood donors who are negative for hepatitis B surface antigen, hepatitis C virus (HCV) antibody and human immunodeficiency virus (HIV) antibody. Further, 30 HBV-genotyped samples were tested to evaluate the “in-house” assay’s capacity to detect genotypes prevalent among individuals attending this tertiary care hospital. Results: The lower limit of detection of this “in-house” HBV real-time PCR was assessed against the WHO international standard and found to be 50 IU/mL. The interassay and intra-assay coefficient of variation (CV) of this “in-house” assay ranged from 1.4% to 9.4% and 0.0% to 2.3%, respectively. Virus loads as estimated with this “in-house” HBV real-time assay correlated well with the commercial artus HBV RG PCR assay (r = 0.95, P < 0.0001). Conclusion: This assay can be used for the detection and accurate quantitation of HBV viral loads in plasma samples. This assay can be employed for the screening of blood donations and can potentially be adapted to a multiplex format for simultaneous detection of HBV, HIV and HCV to reduce the cost of testing in blood banks.

Checklist for optimization and validation of real‐time PCR assays

Real-time polymerase chain reaction (PCR) is a frequently used technique in molecular diagnostics. To date, practical guidelines for the complete process of optimization and validation of commercial and in-house developed molecular diagnostic methods are scare. Therefore, we propose a practical guiding principle for the optimization and validation of real-time PCR assays. Based on literature, existing guidelines, and personal experience, we created a checklist that can be used in different steps of the development and validation process of commercial and in-house developed real-time PCR assays. Furthermore, determination of target values and reproducibility of internal quality controls are included, which allows a statistical follow-up of the performance of the assay. Recently, we used this checklist for the development of various qualitative and quantitative assays for microbiological and hematological applications, for which accreditation according to ISO 15189:2007 was obtained. In our experience, the use of the proposed guidelines leads to a more efficient and standardized optimization and validation. Ultimately, this results in reliable and robust molecular diagnostics. The proposed checklist is independent of environment, equipment, and specific applications and can be used in other laboratories. A worldwide consensus on this kind of checklist should be aimed at.

Evaluation of real-time polymerase chain reaction assays for the detection of herpes simplex virus in swab specimens

An in-house herpes simplex virus (HSV) real-time polymerase chain reaction (PCR) hydrolysis probe assay and three commercial real-time HSV assays were evaluated for the detection of HSV from genital, oral, ocular and dermal clinical samples. Five hundred and sixty samples from patients displaying signs and symptoms of HSV infection were used to evaluate the in-house HSV assay. A representative 151 samples were processed using the artus HSV-1/2 TM PCR Kit, SmartCycler Non-typing and SmartCycler Typing ASR kits. The in-house PCR assay demonstrated an overall positivity rate of 38% (211/560), equating to a 14% increase in HSV detection compared to 24% for culture (135/560). All 76 culture-negative, in-house PCR-positive samples were confirmed using at least one HSV commercial kit. The in-house, SmartCycler Non-typing, artus and SmartCycler Typing assays showed improved sensitivity (100%, 100%, 98% and 99%, respectively) compared to culture (37%), and all real-time assays were highly specific (100%). The in-house and commercial real-time HSV PCR assays performed well and, combined with careful clinical interpretation, should improve the detection, differentiation and quantification of HSV from mucocutaneous swab samples.

Validation of Roche LightCycler Epstein-Barr Virus Quantification Reagents in a Clinical Laboratory Setting

Epstein-Barr virus (EBV) is associated with a wide range of benign and malignant diseases, including infectious mononucleosis, lymphoma, posttransplant lymphoproliferative disorder, and nasopharyngeal carcinoma. Measurement of EBV viral load in plasma is increasingly used for rapid assessment of disease status. We evaluated the performance characteristics of an EBV polymerase chain reaction assay that uses commercial reagents and instruments from Roche Diagnostics (Indianapolis, IN). DNA was extracted from plasma using a MagNaPure instrument, and viral load was measured by real-time polymerase chain reaction on a LightCycler. Analyte-specific reagents included primers and hybridization probes targeting the EBV LMP2 gene and a spiked control sequence. Accuracy and reproducibility were established using DNA from three cell lines. The assay was sensitive to approximately 750 copies of EBV DNA per milliliter of plasma and was linear across at least four orders of magnitude. The assay detected EBV DNA in three of five samples from nasopharyngeal carcinoma patients, seven of nine infectious mononucleosis samples, and 34/34 samples from immunosuppressed patients with clinically significant EBV-related disease, whereas EBV DNA was undetectable in plasma from 21 individuals without EBV-related disease. In conclusion, this LightCycler EBV assay is rapid, sensitive, and linear for quantifying EBV viral load. The assay appears to be useful for measuring clinically significant EBV levels in immunodeficient patients.

Evaluation of Polymerase Chain Reaction for Group B Streptococcus Detection Using an Improved Culture Method

The administration of antibiotic prophylaxis to laboring women who harbor Group B streptococci (GBS) depends on identification of carriers. We sought to evaluate the diagnostic accuracy of real-time polymerase chain reaction (PCR) for detection of GBS using a more stringent culture method. Two swabs were used simultaneously to obtain rectovaginal GBS samples from consenting women. One swab was analyzed using a stringent, validated culture technology, which included direct plating onto selective agar and inoculation of a selective broth. The other swab was used for a commercial real-time PCR assay, which uses amplification to detect the presence of the cfb gene sequence of GBS DNA. We calculated the assay accuracy using sensitivity and specificity. A total of 233 samples were available. Both the culture and PCR methods were positive for 59 and negative for 157 patients. The culture method was positive and PCR was negative in 9 patients. The culture was negative and the PCR positive for 8 patients. The sensitivity of the PCR assay was 86.8% and specificity was 95.2%. The positive predictive value was 88.1% and the negative predictive value was 94.6%. Although a rapid PCR assay may be useful to determine GBS status in the urgent intrapartum setting, the false-negative rate of 13.2% for the real-time PCR assay prohibits its use for standard GBS screening in the office.

Presence of Hepatitis C Virus (HCV) RNA in the Genital Tracts of HCV/HIV‐1–Coinfected Women

Hepatitis C virus (HCV)-infected women--in particular, those coinfected with human immunodeficiency virus type 1 (HIV-1)--can transmit infection to their children and sex partners. The present study was conducted to analyze the presence of HCV RNA in cervicovaginal lavage (CVL) fluid from 71 women (58 HCV/HIV-1-coinfected women and 13 HCV-infected, HIV-1-uninfected women) enrolled in the Women's Interagency HIV Study. HCV RNA was detected (by a commercial polymerase chain reaction assay) in CVL fluid from 18 (29%) of the HIV-1-infected women and from none of the HIV-1-uninfected women (P<.05). Multivariate analysis revealed that risk factors for the presence of HCV RNA in CVL fluid were HCV viremia (odds ratio [OR], 16.81; P=.02) and HIV-1 RNA in CVL fluid (OR, 19.87; P=.02). This observation suggests local interactions between HIV-1 and HCV in the genital tract compartment. There was no correlation between HCV RNA in CVL fluid and CD4, CD8, or CD3 cell counts, HIV-1 RNA viremia, the number of leukocytes in CVL fluid, or HIV-1 therapy. Furthermore, in 3 of 5 analyzed patients who had a detectable CVL HCV RNA load, we found viral variants differing in the 5' untranslated region that were present neither in plasma nor in peripheral-blood mononuclear cells. Our observations point to the importance of the genital tract compartment, in which local HCV replication could be facilitated by local HIV-1 replication.

Diagnostic testing for HIV type 1 RNA in seronegative blood.

We studied the feasibility of routine diagnostic testing for HIV-1 RNA at a publicly funded testing site. HIV-1 RNA was determined with a commercial polymerase chain reaction assay in pooled seronegative blood samples submitted for HIV testing to a public health laboratory. Recovery of HIV-1 RNA from the samples was estimated as at least 8% of viral RNA that was found in freshly prepared plasma. We estimated that screening for HIV-1 RNA in serum pools would result in the identification of blood specimens from more than 95% of acutely infected patients. The frequency of HIV-1 RNA in seronegative blood samples was estimated to be between 19 and 601 per 10(6) submitted specimens. The ratio of HIV-1 RNA positive and seronegative samples to specimens with HIV-1 antibodies confirmed by Western blot was estimated to be between 0.2% and 6.6%. The reagent costs for identifying 1 HIV-infected blood sample were 10-fold higher with the commercially available HIV-1 RNA assay compared with the HIV antibody enzyme-linked immunosorbent assay. Diagnostic testing for HIV-1 RNA may be warranted in high-risk populations since acutely infected patients may benefit most from anti-retroviral therapy and are thought to contribute disproportionately to the HIV epidemic.

Lowering the cut off value of an automated chlamydia enzyme immunoassay and confirmation by PCR and direct immunofluorescent antibody test.

AIMS: To increase the sensitivity of an automated chlamydia enzyme immunoassay by significantly lowering its cut off value, and to maintain specificity by confirmation with polymerase chain reaction (PCR) and...

Evaluation of a commercial polymerase chain reaction assay for the detection of Chlamydia trachomatis

Cell culture has traditionally been considered the most sensitive method for detecting Chlamydia trachomatis from clinical specimens, but depends upon the organisms being viable at the time of cell inoculation. Furthermore, cell culture is slow and labor intensive. Even when a special transport medium is used, there is a progressive loss of viability of C. trachomatis during transport. The detection of C. trachomatis by cell culture is more rapid when immunofluorescence is used to detect early antigen, but requires considerable experience to interpret. The Amplicor™ C. trachomatis system is a commercial polymerase chain reaction (PCR)-based assay combined with nucleic acid hybridization for the direct detection of C. trachomatis in urine and swabs of appropriate sites, with results available within 6 h. All specimens for C. trachomatis received by the Royal Perth Hospital Department of Microbiology during the period 1 July 1994 to 30 June 1995 that were suitable for culture and Amplicor™ PCR were tested by both methods (2029 specimens). Discordant results were obtained in nine cases and were resolved by additional testing. Seventy-one specimens were confirmed as true positives, of these Amplicor™ PCR correctly detected 67 (sensitivity 94.4%) and culture correctly detected 62 (sensitivity 87.3%). The Amplicor™ PCR assay was found to be more sensitive and as specific as culture. It had the added advantages of ease of use, rapid availability of results, standardization and was more suited than culture to processing large numbers of specimens.