Gen-Probe APTIMA Combo Research Articles

P1-S2.14 Neisseria gonorrhoea and Chlamydia trachomatis Re-infection and associated risk factors among cohort of female sex workers in India

BackgroundNeisseria gonorrhoea (NG) and Chlamydia trachomatis (CT) infections can be completely cured by appropriate medication. Syndromic STI management often fails to cover asymomatic NG/CT infections. Additionally, Female sex workers (FSWs),...

P1-S2.54 Repeat Gonococcal and chalymadial infections in a cohort of men who have sex with men in India

BackgroundMen who have sex with men (MSM) are found to be at increased risk for many sexually transmitted infections (STI). Among the STIs, most common are bacterial STIs such as...

O3-S3.05 Chlamydia trachomatis detection by nucleic acid amplification assay using rectal swabs

BackgroundRectal infection with C trachomatis (CT) is increasing in many settings; however, there are currently no FDA approved NAAT for use with rectal specimens. Access to reliable diagnostics using rectal...

P5-S6.19 Prevalence and incidence of sexually transmitted infections among female sex workers in two cities in India: implications for STI control strategies

BackgroundIndia is a large country with marked heterogeneity in prevalence of sexually transmitted infections (STIs) which has implications for STI control strategies. The study objective was to measure the prevalence...

Comparison of the Abbott RealTi m e CT New Formulation Assay with Two Other Commercial Assays for Detection of Wild-Type and New Variant Strains of Chlamydia trachomatis

In an analytical-method comparison study of clinical samples, the Abbott RealTime CT new formulation assay (m2000 real-time PCR), consisting of a duplex PCR targeting different parts of the cryptic plasmid in Chlamydia trachomatis, was compared both with version 2 of the Roche Cobas TaqMan CT assay, comprising a duplex PCR for a target in the cryptic plasmid and the omp1 gene, and with the Gen-Probe Aptima Combo 2 assay (AC2) targeting the C. trachomatis 23S rRNA molecule. First-catch urine samples from Sweden were tested in Malmö, Sweden, for C. trachomatis with the m2000 real-time PCR assay and with an in-house PCR for the new variant C. trachomatis strain with a deletion in the cryptic plasmid. Aliquots of the urine samples were sent to Aarhus, Denmark, where they were further examined with the TaqMan CT and AC2 assays. A positive prevalence of 9.1% (148/1,632 urine samples examined) was detected according to the combined reference standard. The sensitivities and specificities of the three assays were as follows: for the Abbott m2000 assay, 95.3% (141/148) and 99.9% (1,483/1,485), respectively; for the Roche TaqMan assay, 82.4% (122/148) and 100.0% (1,485/1,485); and for the Gen-Probe AC2 assay, 99.3% (147/148) and 99.9% (1,484/1,485). The plasmid mutant strain was detected in 24% (36/148) of the C. trachomatis-positive samples. There is a difference in sensitivity between the new formulations of the Abbott and the Roche assays, but both assays detected the wild-type and new variant C. trachomatis strains equally well.

Nucleic Acid Amplification Tests for Diagnosis of Neisseria gonorrhoeae Oropharyngeal Infections

The optimal methods for the diagnosis of pharyngeal Neisseria gonorrhoeae infection are uncertain. The objective of this study was to define the performance of culture and nucleic acid amplification tests (NAATs) for the diagnosis of pharyngeal N. gonorrhoeae. In this cross-sectional study, males and females >15 years old who acknowledged performing fellatio or cunnilingus (in the previous 2 months) were recruited from three clinics (two human immunodeficiency virus clinics and one sexually transmitted diseases clinic) located in Birmingham, AL. The test performance of culture for N. gonorrhoeae, the Gen-Probe Aptima Combo 2 transcription-mediated amplification assay (TMA), the BD ProbeTec ET amplified DNA strand displacement assay (SDA), and the Roche Cobas Amplicor PCR was defined by using a rotating "gold standard" of any positive results by two or three of the three tests that excluded the test being evaluated. A total of 961 evaluable test sets were collected. On the basis of a rotating gold standard of positive results by two of three comparator tests, the sensitivity and the specificity were as follows: culture for N. gonorrhoeae, 50.0% and 99.4%, respectively; PCR, 80.3% and 73.0%, respectively; TMA, 83.6% and 98.6%, respectively; and SDA, 93.2% and 96.3%, respectively. On the basis of a rotating gold standard of positive results by three of three comparator tests, the sensitivity and specificity were as follows: culture for N. gonorrhoeae, 65.4% and 99.0%, respectively; PCR, 91.9% and 71.8%, respectively; TMA, 100% and 96.2%, respectively; and SDA, 97.1% and 94.2%, respectively. In conclusion, currently available NAATs are more sensitive than culture for the detection of pharyngeal gonorrhea in at-risk patients. PCR is substantially less specific than culture, TMA, or SDA and should not be used for the detection of pharyngeal gonorrhea.

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.

Nucleic Acid Amplification Tests in the Diagnosis of Chlamydial and Gonococcal Infections of the Oropharynx and Rectum in Men Who Have Sex With Men

Several nucleic acid amplification tests (NAATs) are US Food and Drug Administration-cleared for detecting urogenital Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) infection, but they have not been adequately evaluated for the relatively common oropharyngeal or rectal CT and GC infections in men who have sex with men (MSM). Multiple swabs were collected from the oropharynx and rectum of MSM attending a city sexually transmitted disease clinic. The specimens were tested by standard culture and the following NAATs: Roche's Amplicor (PCR), Becton Dickinson's ProbeTec (SDA), and Gen-Probe's APTIMA Combo 2 (AC2) for the detection of CT and GC. Confirmatory testing of specimens with discrepant results was done by NAATs using alternate primers. A total of 1110 MSM were enrolled. Based on initial findings on 205 MSM, PCR had a 78.9% GC specificity with oropharyngeal swabs. Thus, we discontinued PCR testing for the rest of the study. For oropharyngeal GC (89 infections detected), sensitivities were 41% for culture, 72% for SDA, and 84% for AC2. For rectal GC (88 infections detected), sensitivities were 43% for culture, 78% for SDA and 93% for AC2. For oropharyngeal CT (9 infections detected), sensitivities were 44% for culture, 67% for SDA, and 100% for AC2. For rectal CT (68 infections detected), sensitivities were 27% for culture, 63% for SDA, and 93% for AC2. Specificities of SDA and AC2 were > or =99.4% for both organisms and anatomical sites. AC2 and SDA were far superior to culture for the detection of CT or GC from the oropharynx and rectum with AC2 detecting twice as many infections as culture. Further analyses with larger pharyngeal samples are needed, but clearly NAATs can improve our ability to diagnose rectal and oropharyngeal infection with CT or GC in MSM.

The Microbicide Tenofovir Does Not Inhibit Nucleic Acid Amplification Tests for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Urine Samples

The potential inhibitory effects of tenofovir and a placebo were examined using the Becton Dickinson ProbeTec, Gen-Probe Aptima Combo 2, and Roche Amplicor tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae. Concentrations of 5% to 0% of tenofovir and the placebo were added to dilutions of C. trachomatis and N. gonorrhoeae. No appreciable inhibition was observed.

Comparison of APTIMA COMBO 2 assay with polymerase chain reaction Roche assay for detection of Chlamydia trachomatis in endocervical swabs

In the last decade of the past century the incidence rates of sexually transmitted diseases increased dramatically in Russia and the former Soviet Union countries. Chlamydia trachomatis infection is among the most widespread sexually transmitted infection (STI) in Russia; however incidence rates are based mostly on direct immunofluorescence assay and immunoenzyme assay. The prevalence of C. trachomatis infection in Russia has not yet been studied. Molecular diagnostic tests based on nucleic acid amplification technologies have become widely established in clinical microbiology laboratories in recent years. A number of nucleic acid amplification tests are commercially available for detection of C. trachomatis infection. However there are some limitations of their use due to inhibitors of amplification in these assays. The Gen-Probe APTIMA COMBO 2 assay (AC2) (Gen-Probe Incorporated San Diego CA USA) is a recently developed nucleic acid amplification test for detection of C. trachomatis and Neisseria gonorrhoeae. Recent studies showed that AC2 assay is more sensitive than culture direct fluorescentantibody assay and ligase chain reaction assay. (excerpt)

Chlamydia trachomatis RNA in the environment: is there potential for false-positive nucleic acid amplification test results?

Objectives:The ability of molecular methods to detect low levels of nucleic acid has led to the widespread application of techniques based on nucleic acid amplification tests in microbiological diagnosis. This...

The contribution of APTIMA Combo 2 assay to the diagnosis of gonorrhoea in genitourinary medicine setting

For 929 female and 821 male patients attending a genitourinary clinic, samples intended for chlamydia diagnosis were dual tested by nucleic acid amplification for both chlamydia and Neisseria gonorrhoeae (NG). The assay used, Gen-probe APTIMA Combo 2 (AC2) detected all cases of NG found by conventional microscopy and culture. AC2 identified additional patients who had partners with NG, but were themselves negative by microscopy and culture. Few, if any, false-positive AC2 results were found. Use of AC2 increased the number of patients treated for NG. It can reduce the number of specimens required and may limit the need for multiple site testing.

The use and performance of oral–throat rinses to detect pharyngeal Neisseria gonorrhoeae and Chlamydia trachomatis infections

Gonococcal and chlamydial infections in the pharynx can occur as a consequence of oral sex. Currently, diagnosis of these infections typically requires a swab specimen to be collected from the posterior pharynx. However, we assessed the diagnostic adequacy of using commercial mouthwash or water as an oral–throat rinse and subsequent testing with a nucleic acid amplification test (Gen-Probe APTIMA Combo 2 assay; Gen-Probe, San Diego, CA). Mouthwash and water samples, spiked with varying amounts of gonorrhea and chlamydia, remained positive for both organisms for up to 2 weeks after storage at room temperature and 37 °C. A clinical trial compared the test performance of oral–throat rinses to pharyngeal swabs among 561 (250 mouthwash, 311 water) gay and other men who have sex with men. Participants were also surveyed to assess the acceptability, preference, and feasibility of oral–throat rinses in a clinical setting. The prevalence of pharyngeal gonorrhea and chlamydia were 9.5% (53/556) and 1.4% (8/561), respectively. Compared with the pharyngeal swab, mouthwash oral–throat rinses had a sensitivity and specificity for the detection of gonorrhea of 72% and 99.1%, respectively, whereas water had 82% and 99.7%, respectively. Chlamydia prevalence was too low for reliable assessments of test performance. Study participants found oral–throat rinses acceptable, preferable, and feasible when compared with pharyngeal swabs. Further study is needed to investigate discordant results and improve the sensitivity of oral–throat rinses.

Selective Testing Criteria for Gonorrhea among Young Women Screened for Chlamydial Infection: Contribution of Race and Geographic Prevalence

Selective screening criteria have been widely implemented for genital Chlamydia trachomatis (CT) infections but have rarely been developed for Neisseria gonorrhoeae (GC) infection. Women tested for CT in Washington State Infertility Prevention Project clinics in 2003 were also tested for GC using the Gen-Probe APTIMA COMBO 2 TMA assay. We derived 3 sets of selective testing criteria (STC) for gonorrhea, incorporating risk factors identified using logistic regression (STC-1), self-identified race (STC-2), and local rates of gonorrhea in men (STC-3). Of 55,781 women, 173 (0.3%) tested positive for GC. STC-1 included exposure to sexually transmitted diseases, presumptive CT treatment at screening, a pregnancy-related visit, report of a symptomatic partner, dysuria, abnormal vaginal discharge, or a new sex partner during the preceding 60 days. These criteria identified 80% of cases while testing 47% of women. STC-2 added race (black/Native American) to STC-1 and identified 89% of cases while testing 52%. STC-3 added clinic location in a ZIP code area with male urethral GC infection rates in the top quartile of Washington State rates to STC-1 and identified 86% of cases while testing 58%. Although testing criteria incorporating race were most specific, criteria including local area rates of GC infection in men had similar sensitivity and required testing only slightly more women.

Characteristics of the m 2000 Automated Sample Preparation and Multiplex Real-Time PCR System for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae

We evaluated a new real-time PCR-based prototype assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae developed by Abbott Molecular Inc. This assay is designed to be performed on an Abbott m2000 real-time instrument system, which consists of an m2000sp instrument for sample preparation and an m2000rt instrument for real-time PCR amplification and detection. The limit of detection of this prototype assay was determined to be 20 copies of target DNA for both C. trachomatis and N. gonorrhoeae, using serially diluted linearized plasmids. No cross-reactivity could be detected when 55 nongonococcal Neisseria isolates and 3 non-C. trachomatis Chlamydia isolates were tested at 1 million genome equivalents per reaction. Concordance with the Roche Amplicor, BDProbeTec ET, and Gen-Probe APTIMA Combo 2 tests was assessed using unlinked/deidentified surplus clinical specimens previously analyzed with these tests. For C. trachomatis, concordance for positive results ranged from 93.7% to 100%, while concordance for negative results ranged from 98.2% to 100%. For N. gonorrhoeae, concordance for positive and negative results ranged from 91.4% to 100% and 99.3% to 100%, respectively. A workflow analysis of the prototype assay was conducted to obtain information on throughput under laboratory conditions. At 48 samples/run, the time to first result for both C. trachomatis and N. gonorrhoeae was 4.5 h. A total of 135 patient specimens could be analyzed in 8.9 h, with 75 min of hands-on time. This study demonstrated the technical and clinical feasibility of the new Abbott real-time PCR C. trachomatis/N. gonorrhoeae assay.

Supplemental Testing Is Still Required in Australia for Samples Positive for Neisseria gonorrhoeae by Nucleic Acid Detection Tests

Supplemental Testing Is Still Required in Australia for Samples Positive for <i>Neisseria gonorrhoeae</i> by Nucleic Acid Detection Tests

Comparison of the Gen-Probe APTIMA Combo 2 Assay to the AMPLICOR CT/NG Assay for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Urine Samples from Australian Men and Women

The performance of the APTIMA Combo 2 assay (AC2) for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae infections in urine samples was compared to that of the AMPLICOR CT/NG assay (AMP). The AC2 performance was superior to that of AMP for both organisms in this study.

In vitro assessment of the APTIMA Combo 2 assay for the detection of Chlamydia trachomatis using highly purified elementary bodies

The Gen-Probe APTIMA Combo 2 assay has previously been reported to have a high sensitivity. The end point of this assay was evaluated using highly purified chlamydial elementary bodies (EBs). The performance of the APTIMA Combo 2 assay was compared with a commercially available PCR kit, AMPLICOR Chlamydia trachomatis. The number of inclusions of C. trachomatis at the end point of the APTIMA Combo 2 assay was 0.005 inclusion-forming units (i.f.u.) ml(-1), which was equivalent to 0.008 EBs per assay. The end point of the AMPLICOR kit was 5 i.f.u. ml(-1) (equivalent to 0.5 EB per assay). The efficacy of the AMPLICOR C. trachomatis assay was inhibited by phosphate or Fe2+ ion, while these had no effect on the APTIMA Combo 2 assay. In conclusion, the APTIMA Combo 2 assay appears to have a greater sensitivity than the AMPLICOR C. trachomatis assay for detection of C. trachomatis, while demonstrating few problems with inhibitory substances such as phosphate and Fe2+ ion.

Positive Predictive Value of Gen-Probe APTIMA Combo 2 Testing for Neisseria gonorrhoeae in a Population of Women with Low Prevalence of N. gonorrhoeae Infection

We collected specimens from women who tested positive for Neisseria gonorrhoeae using the Gen-Probe APTIMA Combo 2 (AC2), and we performed confirmatory tests using a nucleic acid amplification test (NAAT) that targets alternate gonococcal nucleic acid sequences. Among 59,664 specimens, 280 (0.47%) had positive results using AC2; 265 of these specimens were tested using the confirmatory NAAT, of which 258 yielded positive results (positive predictive value, 97.4%; 95% confidence interval, 95.1%-98.8%). Routine confirmatory testing of specimens with positive AC2 gonorrhea test results is not indicated.