Strand Displacement Amplification Assay Research Articles

Prevalence of sexually transmitted infections in female clinic attendees in Honiara, Solomon Islands

ObjectivesThis study sought to determine the prevalence of common bacterial sexually transmitted infections, including Chlamydia trachomatis and Neisseria gonorrhoeae, in women attending clinics in the Solomon Islands.MethodsWe conducted a sexual...

Evaluation of strategies for confirming Neisseria gonorrhoeae nucleic acid amplification tests

The implementation of widespread unselected screening for Neisseria gonorrhoeae in England, using nucleic acid amplification tests (NAATs), has raised concerns regarding the potential increase in misdiagnoses. To increase the positive predictive value, confirmatory testing of positive specimens has been recommended; however, in practice this can be difficult to perform. This study examined the role of two different testing strategies for confirming the N. gonorrhoeae status of specimens that had been examined by the ProbeTec Strand Displacement Amplification (SDA) assay (Becton Dickinson). A total of 227 residual clinical specimens in SDA assay collection tubes were sent for confirmatory testing using two different testing approaches: (i) examination using two in-house real-time PCR assays (opa and porA pseudogene) and (ii) examination using the APTIMA Combo 2 (AC2) assay and the APTIMA Monospecific N. gonorrhoeae (AGC) tests (Gen-Probe). Of the 113 SDA-positive specimens (including low positives) examined, 93 % were confirmed as N. gonorrhoeae-positive using either one or both real-time PCR assays. In contrast, only 34 % were confirmed using the AC2 and/or the AGC assays. All 114 SDA-negative specimens were confirmed as negative using all four confirmatory tests. Clearly the AC2 and AGC assays cannot reliably be used to confirm residual specimens in SDA assay transportation buffers, due to the incompatibility of different platform chemistries. Although high rates of confirmation (93 %) can be achieved when examining residual SDA assay specimens using independent real-time PCR assays, establishing well-validated in-house real-time PCR assays for diagnostic use is a large undertaking for many primary laboratories and so such tests may be better confined to specialist laboratory services.

New point of care Chlamydia Rapid Test—bridging the gap between diagnosis and treatment: performance evaluation study

Objective To evaluate the performance of a new Chlamydia Rapid Test with vaginal swab specimens as a potential tool for chlamydia diagnosis and screening.Design Performance evaluation study.Settings A young people’s...

Prevalence of Neisseria gonorrhoeae infection in young subjects attending community clinics in South London

Objectives:To describe the prevalence and epidemiology of gonococcal infection in young subjects attending community clinics in South-East London.Methods:Subjects <25 years of age participating in the National Chlamydia Screening Programme were...

A Fast Real-Time Polymerase Chain Reaction Method for Sensitive and Specific Detection of the Neisseria gonorrhoeae porA Pseudogene

Ever since the advent of molecular methods, the diagnostics of Neisseria gonorrhoeae has been troubled by false negative and false positive results compared with culture. Commensal Neisseria species and Neisseria meningitidis are closely related to N. gonorrhoeae and may cross-react when using molecular tests comprising too-low specificity. We have devised a real-time polymerase chain reaction (PCR), including an internal amplification control, that targets the N. gonorrhoeae porA pseudogene. DNA was automatically isolated on a BioRobot M48. Our subsequent PCR method amplified all of the different N. gonorrhoeae international reference strains (n = 34) and N. gonorrhoeae clinical isolates (n = 176) but not isolates of the 13 different nongonococcal Neisseria species (n = 68) that we tested. Furthermore, a panel of gram-negative bacterial (n = 18), gram-positive bacterial (n = 23), fungal (n = 1), and viral (n = 4) as well as human DNA did not amplify. The limit of detection was determined to be less than 7.5 genome equivalents/PCR reaction. In conclusion, the N. gonorrhoeae porA pseudogene real-time PCR developed in the present study is highly sensitive, specific, robust, rapid and reproducible, making it suitable for diagnosis of N. gonorrhoeae infection.

Prospective evaluation of BDProbeTec strand displacement amplification (SDA) system for diagnosis of tuberculosis in non-respiratory and respiratory samples

Nucleic acid amplification techniques (NAATs) have been demonstrated to make significant improvements in the diagnosis of tuberculosis (TB), particularly in the time to diagnosis and the diagnosis of smear-negative TB. The BD ProbeTec strand displacement amplification (SDA) system for the diagnosis of pulmonary and non-pulmonary tuberculosis was evaluated. A total of 689 samples were analysed from patients with clinically suspected TB. Compared with culture, the sensitivity and specificity for pulmonary samples were 98 and 89 %, and against final clinical diagnosis 93 and 92 %, respectively. This assay has undergone limited evaluation for non-respiratory samples and so 331 non-respiratory samples were tested, identifying those specimens that were likely to yield a useful result. These were CSF (n = 104), fine needle aspirates (n = 64) and pus (n = 41). Pleural fluid (n = 47) was identified as a poor specimen. A concern in using the SDA assay was that low-positive samples were difficult to interpret; 7.8 % of specimens fell into this category. Indeed, 64 % of the discrepant results, when compared to final clinical diagnosis, could be assigned as low-positive samples. Specimen type did not predict likelihood of a sample being in the low-positive zone. Although the manufacturers do not describe the concept of a low-positive zone, we have found that it aids clinical diagnosis.

Evaluation of the BDProbeTec strand displacement amplification assay in comparison with the AMTD II direct test for rapid diagnosis of tuberculosis

The BDProbeTec MTB assay for direct detection of Mycobacterium tuberculosis was evaluated in comparison with the AMTD-II assay on 94 samples from different patients with clinical suspicion of tuberculosis. Using a combination of culture on Lowenstein-Jensen medium (with or without preculture in BACTEC 9000) and clinical diagnosis as the standard, BDProbeTec MTB showed high sensitivity and specificity (96.1% and 100%, respectively), similar to AMTD-II (96.1% and 97.1%, respectively), with significantly higher sensitivity than the Ziehl-Neelsen stain for acid-fast bacilli (73%, p < 0.05).

Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by strand displacement amplification and relevance of the amplification control for use with vaginal swab specimens.

Vaginal swab specimens may be preferable to cervical swab or urine specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae because of the ease of specimen collection and transport. The purpose of this study was to evaluate whether vaginal swab specimens are equivalent to cervical swab specimens for the detection of N. gonorrhoeae and C. trachomatis by the Becton Dickinson strand displacement amplification assay (SDA) with the BDProbeTec ET instrument and then to evaluate the use of the amplification control in a clinical research setting. In the first phase, vaginal and cervical swab specimens were obtained from 455 symptomatic women aged 18 to 40 attending primary health care and sexually transmitted disease clinics. Thirty-nine specimens (8.6%) had true-positive results for N. gonorrhoeae and 37 specimens (8.1%) had true-positive results for C. trachomatis. The sensitivity of SDA was superior to that of culture for the detection of N. gonorrhoeae with vaginal swab specimens and equivalent to that of the Roche PCR for the detection of C. trachomatis with cervical swab specimens. In the second phase of the study, 1,411 consecutively collected vaginal swab specimens were evaluated, with 357 (25.3%) specimens giving indeterminate readings on the basis of the result for the amplification control. The prevalences of sexually transmitted pathogens in vaginal swab specimens with and without use of the amplification control were 6.0 and 5.8%, respectively, for C. trachomatis and 3.1 and 3.0%, respectively, for N. gonorrhoeae. Although, vaginal swab specimens were equivalent to cervical swab specimens for the detection of N. gonorrhoeae and C. trachomatis by SDA with respect to sensitivity, one in four vaginal swab specimens yielded an indeterminate result when the amplification control was used. The amplification control has limited value for use with vaginal swab specimens.