Enhancing the specificity of the COBAS AMPLICOR CT/NG test for Neisseria gonorrhoeae by retesting specimens with equivocal results

Improving gonorrhoea molecular diagnostics: Genome mining-based identification of identical multi-repeat sequences (IMRS) in Neisseria gonorrhoeae

Background

Curable sexually transmitted infections (STIs), such as Neisseria gonorrhoeae (N. gonorrhoeae), are a major cause of poor pregnancy outcomes. The infection is often asymptomatic in pregnant women, and a syndrome-based approach of testing leads to a missed diagnosis. Culture followed by microscopy is inadequate and time-consuming. The gold standard nucleic acid amplification tests require advanced infrastructure settings, whereas point-of-care tests are limited to immunoassays with sensitivities and specificities insufficient to accurately diagnose asymptomatic cases. This necessitates the development and validation of assays that are fit for purpose.

Methods

We identified new diagnostic target biomarker regions for N. gonorrhoeae using an algorithm for genome mining of identical multi-repeat sequences (IMRS). These were then developed as DNA amplification primers to design better diagnostic assays. To test the primer pair, genomic DNA was 10-fold serially diluted (100 pg/μL to 1 × 10-3 pg/μL) and used as DNA template for PCR reactions. The gold standard PCR using 16S rRNA primers was also run as a comparative test, and both assay products were resolved on 1% agarose gel.

Results

Our newly developed N. gonorrhoeae IMRS-PCR assay had an analytical sensitivity of 6 fg/μL representing better sensitivity than the 16S rRNA PCR assay with an analytical sensitivity of 4.3096 pg/μL. The assay was also successfully validated using clinical urethral swab samples. We further advanced this technique by developing an isothermal IMRS, which was both reliable and sensitive for detecting cultured N. gonorrhoeae isolates at a concentration of 38 ng/μL. Combining isothermal IMRS with a low-cost lateral flow assay, we were able to detect N. gonorrhoeae amplicons at a starting concentration of 100 pg/μL.

Conclusion

Therefore, there is a potential to implement this concept within miniaturized, isothermal, microfluidic platforms, and laboratory-on-a-chip diagnostic devices for highly reliable point-of-care testing.

Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae--2014

This report updates CDC's 2002 recommendations regarding screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections (CDC. Screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections-2002. MMWR 2002;51[No. RR-15]) and provides new recommendations regarding optimal specimen types, the use of tests to detect rectal and oropharyngeal C. trachomatis and N. gonorrhoeae infections, and circumstances when supplemental testing is indicated. The recommendations in this report are intended for use by clinical laboratory directors, laboratory staff, clinicians, and disease control personnel who must choose among the multiple available tests, establish standard operating procedures for collecting and processing specimens, interpret test results for laboratory reporting, and counsel and treat patients. The performance of nucleic acid amplification tests (NAATs) with respect to overall sensitivity, specificity, and ease of specimen transport is better than that of any of the other tests available for the diagnosis of chlamydial and gonococcal infections. Laboratories should use NAATs to detect chlamydia and gonorrhea except in cases of child sexual assault involving boys and rectal and oropharyngeal infections in prepubescent girls and when evaluating a potential gonorrhea treatment failure, in which case culture and susceptibility testing might be required. NAATs that have been cleared by the Food and Drug Administration (FDA) for the detection of C. trachomatis and N. gonorrhoeae infections are recommended as screening or diagnostic tests because they have been evaluated in patients with and without symptoms. Maintaining the capability to culture for both N. gonorrhoeae and C. trachomatis in laboratories throughout the country is important because data are insufficient to recommend nonculture tests in cases of sexual assault in prepubescent boys and extragenital anatomic site exposure in prepubescent girls. N. gonorrhoeae culture is required to evaluate suspected cases of gonorrhea treatment failure and to monitor developing resistance to current treatment regimens. Chlamydia culture also should be maintained in some laboratories to monitor future changes in antibiotic susceptibility and to support surveillance and research activities such as detection of lymphogranuloma venereum or rare infections caused by variant or mutated C. trachomatis.

DNA detection and seroprevalence of human papillomavirus in a cohort of adolescent women

OBJECTIVES

Human papillomavirus (HPV) infections are common in adolescent women, while the rare cancerous sequelae of HPV infections do not generally occur until the 4th or 5th decades of life. This prospective study of a cohort of adolescent women was performed to further our knowledge of the natural history of incident and prevalent HPV infections.

METHODS

Self-vaginal swabs collected from high-risk, unvaccinated adolescent women in a longitudinal study were analysed for HPV DNA. Sera were collected at enrolment and later tested for HPV antibodies. Statistical analysis was performed to determine the HPV genotype distribution and duration of detection, and to determine rates of seropositivity and seroconversion for HPV types represented in the assays.

RESULTS

146 subjects (mean enrolment age=15.4 years; mean duration of follow-up=5.8 years) had samples adequate for analysis of HPV detection, and 95 of these subjects had paired sera available. The cumulative prevalence for high-risk and low-risk HPV types was 95.9% and 91.1%, respectively. HPV types 6, 11, 16 and 18 (HPV types represented in the quadrivalent vaccine) were found at some point in 40.4%, 6.2%, 48% and 24% of participants, respectively. Serological data confirmed exposure to these vaccine-covered types, as well as to other high-risk HPV types.

CONCLUSIONS

In this cohort of adolescent women, high- and low-risk HPV types were frequently detected, and serological data confirmed exposure in most subjects. The high-prevalence HPV types represented in the quadrivalent HPV vaccine further support vaccination of women at an age well before sexual debut.

Development and evaluation of a next-generation digital PCR diagnostic assay for ocular Chlamydia trachomatis infections

Droplet digital PCR (ddPCR) is an emulsion PCR process that performs absolute quantitation of nucleic acids. We developed a ddPCR assay for Chlamydia trachomatis infections and found it to be accurate and precise. Using PCR mixtures containing plasmids engineered to include the PCR target sequences, we were able to quantify with a dynamic range between 0.07 and 3,160 targets/μl (r² = 0.9927) with >95% confidence. Using 1,509 clinical conjunctival swab samples from a population in which trachoma is endemic in Guinea Bissau, we evaluated the specificity and sensitivity of the quantitative ddPCR assay in diagnosing ocular C. trachomatis infections by comparing the performances of ddPCR and the Roche Amplicor CT/NG test. We defined ddPCR tests as positive when we had ≥95% confidence in a nonzero estimate of target load. The sensitivity of ddPCR against Amplicor was 73.3% (95% confidence interval [CI], 67.9 to 78.7%), and specificity was 99.1% (95% CI, 98.6 to 99.6%). Negative and positive predictive values were 94.6% (95% CI, 93.4 to 95.8%) and 94.5% (95% CI, 91.3 to 97.7%), respectively. Based on Amplicor CT/NG testing, the estimated population prevalence of C. trachomatis ocular infection was ∼17.5%. Receiver-operator curve analysis was used to select critical cutoff values for use in clinical settings in which a balance between higher sensitivity and specificity is required. We concluded that ddPCR is an effective diagnostic technology suitable for both research and clinical use in diagnosing ocular C. trachomatis infections.

HIV and STI prevalence and determinants among male migrant workers in India

BACKGROUND

Our objective was to estimate for the first time the prevalence and determinants of human immunodeficiency virus type 1 (HIV-1) and sexually transmitted infections (STIs) among male migrants in India.

METHODOLOGY/PRINCIPAL FINDINGS

We conducted a multi-stage stratified probability sample survey of migrant (defined as not born in Surat city) men aged 18 to 49 years working in the diamond and textile industries in Surat city. Behavioural and biological data were collected. Biological data included laboratory diagnosed herpes simplex virus type 2 (HSV-2), syphilis, chlamydia, gonorrhoea, Trichomonas vaginalis (together defined as 'any STI') and HIV-1. Likely recently acquired STIs included chlamydia, gonorrhoea, T. vaginalis and syphilis with rapid plasma reagin ≥1:8. The response rate was 77% (845/1099). Among 841 participants, HIV-1 prevalence was 1.0%, 'any STI' prevalence was 9.5% and 38.9% of these STIs were likely to have been recently acquired. Being a diamond worker, Surat resident for 10+ years and recent antibiotic use were each associated with higher odds of 'any STI' (aORs 1.83 (95% CI 1.09-3.09), 1.98 (95% CI 1.22-3.22) and 2.57 (95% CI 1 .17-5.64), respectively) after adjusting for the other two factors and age. The main study limitation was social desirability bias for self-reported sexual behaviour; STIs were diagnosed in some self-reported virgins.

CONCLUSIONS/SIGNIFICANCE

HIV and STI prevalence were lower than expected, but prevention interventions remain necessary in Surat since almost 40% of STIs among participants were probably recently acquired and sentinel surveillance HIV prevalence remains high. The participants had a similar HIV prevalence to Surat antenatal clinic attendees, a proxy for the general population. This suggests migrants are not always at higher risk of HIV compared to the general population in their migration destination. Our findings highlight the need to contextualise research findings from a specific setting with other local information to guide HIV/STI prevention interventions.

Prevalence of pharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae among heterosexual men in Japan

Pharyngeal chlamydial and gonococcal infections can occur as a consequence of oral sex, and they also can be transmitted from the pharynx to the genital tract of sex partners. There have been many reports on the prevalence of pharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae in men who have sex with men; however, there have been few reports on the prevalence of these pathogens in the pharynges of heterosexual men. In this study, we determined the prevalence of pharyngeal C. trachomatis and N. gonorrhoeae in 42 heterosexual men diagnosed with urethritis. Pharyngeal swabs and first-voided urine specimens were tested using the Gen-Probe APTIMA Combo 2 transcription-mediated amplification assay. The prevalence of pharyngeal C. trachomatis and N. gonorrhoeae in patients with urethritis was 2.4 % (1/42) and 11.9 % (5/42), respectively. Among patients with either chlamydial or gonococcal urethritis, 9.1 % (1/11) and 25.0 % (5/20) had pharyngeal C. trachomatis or N. gonorrhoeae, respectively. Our results suggest that screening for pharyngeal colonization by N. gonorrhoeae and C. trachomatis using validated nucleic acid amplification tests should be performed in heterosexual men diagnosed with urethritis.

African women recently infected with HIV-1 and HSV-2 have increased risk of acquiring Neisseria gonorrhoeae and Chlamydia trachomatis in the Methods for Improving Reproductive Health in Africa trial

BACKGROUND

Neisseria gonorrhoeae and Chlamydia trachomatis are 2 common causative agents of cervical bacterial sexually transmitted infections (STI). Against the background of the concurrent epidemics of STIs and HIV in sub-Saharan Africa, we examined the effect of HIV-1 and HSV-2 on acquiring N. gonorrhoeae and C. trachomatis in a cohort of southern African women at risk for HIV infection.

METHODS

We examined incidence of first infection with N. gonorrhoeae and C. trachomatis in the multisite randomized controlled trial Methods for Improving Reproductive Health in Africa. Multivariable Cox proportional hazards models with time-dependent covariates were used.

RESULTS

The incidence rates of C. trachomatis and N. gonorrhoeae infections were 6.14 per 100 woman-years and 2.42 per 100 women-years, respectively. In multivariable analyses, women who became infected with HIV-1 were more likely to acquire C. trachomatis (adjusted hazard ratio [adj. HR], 1.86; 95% confidence interval [CI], 1.34-2.57) and N. gonorrhoeae (adj. HR, 2.29; 95% CI, 1.47-3.56) compared with HIV-uninfected women. Similarly, HSV-2 infected women were more likely to acquire C. trachomatis (adj. HR, 1.29; 95% CI, 1.05-1.58) and N. gonorrhoeae (adj. HR, 1.57; 95% CI, 1.11-2.21). Women who were of younger age, who did not live with their primary male partner, and who changed sex partners during the study were also more likely to acquire a cervical STI.

CONCLUSIONS

Women recently infected with HIV-1 and HSV-2 were at increased risk of acquiring N. gonorrhoeae and C. trachomatis. Proactive screening and treatment of these common cervical infections, particularly among those infected with HIV-1 and HSV-2, should be considered for young sexually active women in settings with a high prevalence of HIV/STIs.

Evaluation of six commercial nucleic acid amplification tests for detection of Neisseria gonorrhoeae and other Neisseria species

Molecular detection of Neisseria gonorrhoeae in extragenital samples may result in false-positive results due to cross-reaction with commensal Neisseria species or Neisseria meningitidis. This study examined 450 characterized clinical culture isolates, comprising 216 N. gonorrhoeae isolates and 234 isolates of nongonococcal Neisseria species (n = 218) and 16 isolates of other closely related bacteria, with six commercial nucleic acid amplification tests (NAATs). The six NAATs tested were Gen-Probe APTIMA COMBO 2 and APTIMA GC, Roche COBAS Amplicor CT/NG and COBAS 4800 CT/NG tests, BD ProbeTec GC Qx amplified DNA assay, and Abbott RealTime CT/NG test. All assays except COBAS Amplicor CT/NG test where four (1.9%) isolates were not detected showed a positive result with all N. gonorrhoeae isolates (n = 216). Among the 234 nongonococcal isolates examined, initial results from all assays displayed some false-positive results due to cross-reactions. Specifically, the COBAS Amplicor and ProbeTec tests showed the highest number of false-positive results, detecting 33 (14.1%) and 26 (11%) nongonococcal Neisseria isolates, respectively. On the first testing, APTIMA COMBO 2, APTIMA GC, Abbott RealTime, and Roche COBAS 4800 showed lower level of cross-reactions with five (2.1%), four (1.7%), two (1%), and two (1%) of the isolates showing low-level positivity, respectively. Upon retesting of these nine nongonococcal isolates using freshly cultured colonies, none were positive by the APTIMA COMBO 2, Abbott RealTime, or COBAS 4800 test. In conclusion, the COBAS Amplicor and ProbeTec tests displayed high number of false-positive results, while the remaining NAATs showed only sporadic low-level false-positive results. Supplementary testing for confirmation of N. gonorrhoeae NAATs remains recommended with all samples tested, in particular those from extragenital sites.

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.

Aptima Combo 2 testing detected additional cases of Neisseria gonorrhoeae infection in men and women in community settings

Aptima Combo 2 (AC2) Neisseria gonorrhoeae testing of 81,405 patients who were tested by culture and 14,666 who were AC2 tested for Chlamydia trachomatis detected 142 extra infections and confirmed 106 culture-positive samples (the positivity rate increased from 0.13 in testing by culture to 0.26 in testing by AC2). Retrievable AC2 positive samples were confirmed (98.5%) by an alternate AGC test.

Direct simultaneous detection of 6 sexually transmitted pathogens from clinical specimens by multiplex polymerase chain reaction and auto-capillary electrophoresis

The availability of a reliable and user-friendly method to identify pathogens causing sexually transmitted diseases (STDs) is essential to reduce the complications and spread of infection. In this study, genital/urinary specimens from 113 patients with STDs were simultaneously tested for 6 pathogens using the automated Seeplex® (Seegene, Seoul, Korea) multiplex polymerase chain reaction (PCR)-based STD6B auto-capillary electrophoresis (ACE) system. The results were compared with conventional reference methods, including culture and PCR tests. The sensitivity of STD6B ACE was found to be 100% for Chlamydia trachomatis, Mycoplasma hominis, Mycoplasma genitalium, Neisseria gonorrhoeae, and Trichomonas vaginalis, and 98% for genital Ureoplasma (U. urealyticum and U. parvum). Specificity ranged from 97% to 100%. One pathogen was detected in 51 specimens, and 2 or more pathogens were detected in 24. In conclusion, the multiplex PCR and ACE system is highly sensitive and specific for the rapid, simultaneous detection of STD pathogens directly from a single specimen.

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.

Evaluation of an automated extraction method for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Cobas Amplicor PCR from different sample materials

A commercially available automated device (MagNA Pure LC) was adapted for nucleic acid extraction of urogenital specimen for subsequent PCR detection of Chlamydia trachomatis and Neisseria gonorrhoeae in a clinical laboratory. Results were compared to the standard manual extraction procedure and showed excellent correlation, with even slightly increased sensitivity.

Use of a dual priming oligonucleotide system to detect multiple sexually transmitted pathogens in clinical specimens

AIMS

To evaluate a new dual priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR) assay for detection of six sexually transmitted pathogens, including Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum and Trichomonas vaginalis.

METHODS AND RESULTS

Using 130 clinical specimens, the results obtained by the multiplex PCR, previously established in-house PCR and COBAS Amplicor PCR assays were compared. The specimens frequently contained multiple pathogens (34/130 specimens). The multiplex PCR assay had an overall sensitivity of 96% and specificity of 100% compared to the in-house PCR assay at >20 microg ml(-1) of DNA concentrations in samples and there was no cross-reaction with nonpathogenic Neisseria species that cause the majority of false-positive results with the COBAS Amplicor PCR assay.

CONCLUSIONS

The DPO-based multiplex PCR assay detected the six sexually transmitted pathogens in clinical specimens with a high sensitivity and specificity, although its sensitivity was dependent on the DNA content of the samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

It is the first report about the new DPO-based technique to detect multiple sexually transmitted pathogens in a single assay, which has considerable potential to diagnose the infections accurately and rapidly.

Evaluation of self-collected glans and rectal swabs from men who have sex with men for detection of Chlamydia trachomatis and Neisseria gonorrhoeae by use of nucleic acid amplification tests

Self-collected glans and rectal swab specimens from men who have sex with men (MSM) may be appropriate, convenient specimens for testing. We evaluated the use of self-collected swabs for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by a transcription-mediated amplification test (AC2; Aptima Combo 2; Gen-Probe Inc.) and a strand displacement amplification test (SDA; ProbeTec; Becton Dickinson Co.) in MSM seen at the city sexually transmitted disease clinic in San Francisco, CA. For the glans swab specimen, subjects enrolled early in the study rolled a Dacron swab across the meatus three times (method 1). A slightly more invasive procedure was performed later in the study: the subjects inserted the swab 1/4 in. into the urethra, rotated the swab, and then withdrew the swab (method 2). MSM self-collected a rectal swab specimen and also provided first-catch urine (FCU). Additional rectal swab samples were then obtained by the clinician. For the detection of C. trachomatis and N. gonorrhoeae, all swabs were evaluated by AC2 and SDA, FCU was tested by AC2, and the clinician-collected rectal swabs were cultured. A rectal true-positive (TP) result was defined as a culture-positive result for C. trachomatis or N. gonorrhoeae, two or more positive nucleic acid amplification test (NAAT) results, or a single NAAT-positive result confirmed by an alternate amplification method (the Aptima C. trachomatis or N. gonorrhoeae test). A glans TP result was defined as a positive result for FCU, positive results for both glans specimens (one tested by AC2 and one tested by SDA), or a positive result for a single glans specimen confirmed by an alternate amplification method. The prevalence rates of C. trachomatis and N. gonorrhoeae by testing of FCU were 6.8% (60/882 specimens) and 12.2% (108/882 specimens), respectively. Mixed results were obtained with the glans swab: N. gonorrhoeae detection by AC2 and SDA (method 1) had the best performance (sensitivities, >92%) with samples from a population with a higher prevalence of infection, but their performance for the detection of C. trachomatis was poor and varied by collection method (sensitivities, 56 to 68%). The prevalence rates of C. trachomatis and N. gonorrhoeae in the rectum were 7.3% (66/907 specimens) and 9.4% (83/882 specimens), respectively. The sensitivities of the tests with self-collected and clinician-collected rectal swab specimens were comparable (for C. trachomatis, 41% and 44%, respectively, by SDA and 82% and 71%, respectively, by AC2; for N. gonorrhoeae, 77% and 68%, respectively, by SDA and 84% and 78%, respectively, by AC2). AC2 and SDA were far superior to culture for the detection of C. trachomatis and N. gonorrhoeae in the rectum, with both tests detecting at least twice as many infections. While we found self-collected rectal swabs from MSM to be valid specimens for testing, the sensitivities of the tests with glans swab specimens were disappointing except for those from patients with symptomatic N. gonorrhoeae infections. Self-collected glans swab specimens may not be appropriate for the detection of C. trachomatis or for the detection of N. gonorrhoeae in low-risk or asymptomatic patients by AC2 and SDA, and we would not recommend their use on the basis of our results. Further studies are needed.

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.

The diaphragm and lubricant gel for prevention of cervical sexually transmitted infections: results of a randomized controlled trial

Background

We evaluated the effectiveness of the Ortho All-Flex Diaphragm, lubricant gel (Replens®) and condoms compared to condoms alone on the incidence of chlamydial and gonococcal infections in an open-label randomized controlled trial among women at risk of HIV/STI infections.

Methods

We randomized 5045 sexually-active women at three sites in Southern Africa. Participants who tested positive for curable STIs were treated prior to enrollment as per local guidelines. Women were followed quarterly and tested for Chlamydia trachomatis (CT) or Neisseria gonorrhoeae (GC) infection by nucleic-acid amplification testing (Roche Amplicor®) using first-catch urine specimens. STIs detected at follow-up visits were treated. We compared the incidence of first infection after randomization between study arms in both intent-to-treat (ITT) and per-protocol populations.

Findings

Baseline demographic, behavioral and clinical characteristics were balanced across study arms. Nearly 80% of participants were under 35 years of age. Median follow-up time was 21 months and the retention rate was over 93%. There were 471 first chlamydia infections, 247 in the intervention arm and 224 in the control arm with an overall incidence of 6.2/100 woman-years (wy) (relative hazard (RH) 1.11, 95% Confidence Interval (CI): 0.93–1.33; p = 0.25) and 192 first gonococcal infections, 95 in the intervention arm and 97 in the control arm with an overall incidence of 2.4/100wy (RH 0.98, 95%CI: 0.74–1.30; p = 0.90). Per protocol results indicated that when diaphragm adherence was defined as “always use” since the last visit, there was a significant reduction in the incidence of GC infection among women randomized to the intervention arm (RH 0.61, 95%CI: 0.41–0.91, P = 0.02).

Interpretation

There was no difference by study arm in the rate of acquisition of CT or GC. However, our per-protocol results suggest that consistent use of the diaphragm may reduce acquisition of GC.

Trial Registration

ClinicalTrials.gov NCT00121459 [NCT00121459]

Male circumcision and women's risk of incident chlamydial, gonococcal, and trichomonal infections

BACKGROUND

Male circumcision (MC) decreases the risk of human immunodeficiency virus (HIV) acquisition in men. We explored associations between MC of the primary sex partner and women's risk of acquisition of chlamydial (Ct), gonococcal (GC), or trichomonal (Tv) infections.

METHODS

We analyzed data from a prospective study on hormonal contraception and incident human immunodeficiency virus/sexually transmitted infection (STI) among women from Uganda, Zimbabwe, and Thailand. At enrollment and each follow-up visit, we collected endocervical swabs for polymerase chain reaction identification of Ct and GC; Tv was diagnosed by wet mount. Using Cox proportional hazards models, we compared time to STI acquisition for women according to their partner's MC status.

RESULTS

Among 5925 women (2180 from Uganda, 2228 from Zimbabwe, and 1517 from Thailand), 18.6% reported a circumcised primary partner at baseline, 70.8% reported an uncircumcised partner, and 9.7% did not know their partner's circumcision status. During follow-up, 408, 305, and 362 participants had a first incident Ct, GC, or Tv infection, respectively. In multivariate analysis, after controlling for contraceptive method, age, age at coital debut, and country, the adjusted hazard ratio (HR) comparing women with circumcised partners with those with uncircumcised partners for Ct was 1.25 [95% confidence interval (CI) 0.96-1.63]; for GC, adjusted HR 0.99 (95% CI 0.74-1.31); for Tv, adjusted HR 1.05 (95% CI 0.80-1.36), and for the 3 STIs combined, adjusted HR 1.02 (95% CI 0.85-1.21).

CONCLUSIONS

MC was not associated with women's risk of acquisition of Ct, GC, or Tv infection in this cohort.

Trichomonas vaginalis infection and human immunodeficiency virus acquisition in African women

BACKGROUND

Trichomoniasis vaginalis is the most common nonviral sexually transmitted infection (STI) worldwide, with a particularly high prevalence in regions of human immunodeficiency virus (HIV) endemicity. However, its impact as a cofactor for HIV acquisition is poorly understood.

METHODS

Samples from 213 women who experienced HIV seroconversion (cases) during a longitudinal study involving 4450 women in Uganda and Zimbabwe were matched with samples from HIV-uninfected women (controls). All samples underwent polymerase chain reaction (PCR) analysis for Trichomonas vaginalis DNA. For cases, analyzed samples were from the visit in which HIV seroconversion was detected and the visit preceding detection of seroconversion; for controls, one analyzed sample was from the visit matched by follow-up duration to the cases' seroconversion visit, and the other sample was from the visit immediately preceding the matched visit.

RESULTS

The prevalence of T. vaginalis infection before HIV infection was 11.3% in cases and 4.5% in controls (P = .002). In multivariable analysis controlling for hormonal contraception, other STIs, behavioral, and demographic factors, the adjusted odds ratio for HIV acquisition was 2.74 (95% confidence interval, 1.25-6.00) for T. vaginalis-positive cases. The presence of behavioral risk factors for HIV infection, study recruitment from a referral population at high-risk for HIV, primary sex partner-associated risk for HIV infection, and herpes simplex virus type 2 seropositivity were also predictive of incident HIV infection.

CONCLUSIONS

T. vaginalis infection is strongly associated with an increased risk for HIV infection in this general population of African women. Given the high prevalence of T. vaginalis infection in HIV-endemic areas, T. vaginalis control may have a substantial impact on preventing HIV acquisition among women.

Evaluation of CDC-recommended approaches for confirmatory testing of positive Neisseria gonorrhoeae nucleic acid amplification test results

We evaluated three of the CDC approaches for confirming Neisseria gonorrhoeae (gonococcus [GC])-positive nucleic acid amplification test (NAAT) results: (i) repeating the original test on the original specimen, (ii) testing the original specimen with a different test, and (iii) performing a different test on a duplicate specimen collected at the same visit. For the first approach, clinical specimens were initially tested by Aptima Combo 2 (AC2) (Gen-Probe Inc., San Diego, CA), ProbeTec (strand displacement amplification [SDA]) (Becton Dickinson Co., Sparks, MD), and Amplicor (PCR) (Roche Molecular Systems, Branchburg, NJ). The original GC-positive specimens were then retested by the same NAAT for confirmation. For the second approach, specimens initially positive by AC2, SDA, or PCR were retested by different NAATs (SDA, PCR, AC2, and Aptima Neisseria gonorrhoeae assay [AGC]; Gen-Probe Inc.). For the third approach, duplicate urethral swabs and first-catch urine (FCU) samples from men and duplicate cervical swabs and FCU samples from women were each tested by SDA, AC2, and AGC in parallel. We found that 89 to 96% of samples positive by SDA, PCR, and AC2 were confirmed by repeat testing and that 85 to 98% of SDA, PCR, and AC2 results were confirmed by using different NAATs on the original specimen. For FCU samples from men, any NAAT can be used for confirmation. However, for all other specimen types, some NAATs cannot be used to confirm positive results from other NAATs. Thus, a single repeat test appears to be a reliable method for confirmation, but by doing more extensive testing, an additional 5% were confirmed. With >90% of all GC-positive NAATs being confirmed, our results show that confirmatory testing is not warranted for these genital specimens.

Evaluation of a rapid point-of-care test for the detection of gonococcal infection among female sex workers in Benin

OBJECTIVES

To assess the validity of the PATH (Seattle, Washington, USA) GC-Check rapid test, a point-of-care immunochromatographic strip test, in the detection of gonococcal infection among female sex workers (FSWs) in Benin.

METHODS

Women consulting consecutively at two FSW-dedicated clinics in Cotonou and Porto Novo (Benin) were recruited over three, 1-month periods between October 2003 and July 2004. After written informed consent, participants were administered a short interview and underwent a speculum examination where two cervical swabs were collected (in a subset of women, a vaginal swab was also collected). One cervical swab and the vaginal swab were immediately tested with the rapid test. The other cervical swab was frozen at -20 degrees C for at most four weeks and then transported to Québec (Canada), where it was tested with the Roche Amplicor CT/NG PCR assay. Samples positive for gonococcal infection were confirmed using a 16SrRNA PCR assay.

RESULTS

1084 FSWs (median age 29 years) participated in the study, of whom 50 (4.6%) had a confirmed gonococcal infection. The sensitivity, specificity, positive and negative predictive values of the rapid test on cervical samples were 70.0% (95% confidence interval (CI) 55.4% to 82.1%), 97.2% (95% CI 96.0% to 98.1%), 54.7% and 98.5%, respectively. The sensitivity of the rapid test on vaginal swabs among 759 women (37 positives for gonococcal infection) was significantly lower than with the cervical swab (54.1%, p = 0.008), whereas the specificity was comparable (98.2%, p = 0.13).

CONCLUSIONS

The PATH GC-Check test may be as efficient as a gold standard polymerase chain reaction (PCR) test for treating gonococcal infection when taking into account the proportion of women who do not return for their test results. In clinics serving populations with moderate prevalence of this infection, it could significantly reduce over-treatment compared to the syndromic approach.

Neisseria species identification assay for the confirmation of Neisseria gonorrhoeae-positive results of the COBAS Amplicor PCR

Screening assays for Neisseria gonorrhoeae exhibit low positive predictive values, particularly in low-prevalence populations. A new real-time PCR assay that detects and identifies individual Neisseria spp. using melt curve analysis was compared to two previously published supplementary assays. NsppID, a 16S rRNA real-time PCR/melt curve assay developed to distinguish N. gonorrhoeae from other Neisseria spp., was compared to real-time PCR assays targeting genes reportedly specific for N. gonorrhoeae, the cppB gene and the porA pseudogene. A total of 408 clinical specimens (324 female endocervical swabs and 84 male urine or urogenital swab specimens) were screened using the COBAS Amplicor assay for Chlamydia trachomatis and N. gonorrhoeae (CT/NG) (Roche Diagnostics, Indianapolis, IN) followed by confirmatory testing via real-time PCR. The NsppID assay detected Neisseria spp. in 150/181 COBAS-positive specimens (82%), including six dual infections, and identified N. gonorrhoeae in 102 (56%) specimens. Sixty-nine of 181 (38%) specimens were positive for N. gonorrhoeae by porA pseudogene, and 115/181 (64%) were positive for cppB. However, cppB was also positive in 15% of COBAS-negative specimens, more than either NsppID (4%) or porA pseudogene (2%) assays. The porA pseudogene assay had the highest specificity for both genders but the lowest sensitivity, especially in female specimens. NsppID had a slightly lower specificity but greater sensitivity and overall accuracy. The least desirable confirmatory assay was cppB, due to poor specificity. The NsppID assay is an accurate confirmatory assay for N. gonorrhoeae detection. In addition, the NsppID assay can identify the non-N. gonorrhoeae species responsible for the majority of false-positive results from the COBAS Amplicor CT/NG assay.

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.

Laboratory Markers Carbohydrate-Deficient Transferrin, γ-Glutamyltransferase, and Mean Corpuscular Volume Are Not Useful as Screening Tools for High-Risk Drinking in the General Population: Results From the Study of Health in Pomerania (SHIP)

BACKGROUND

Assessment of high-risk drinking in the general population can be problematic: questionnaire-based instruments may carry the problem of random or systematic recall bias, and the effectiveness of screening of single biomarkers has been shown to be insufficient. In this article, we analyze the alcohol intake/biomarker relationship of carbohydrate-deficient transferrin (CDT), gamma-glutamyltransferase (GGT), and erythrocyte mean corpuscular volume (MCV). Specific aims were (1) screening effectiveness comparison of GGT, CDT, and MCV in terms of sensitivity, specificity, and positive (PPVs) and negative predictive values (NPVs) and the effect of covariates on these measures; (2) the comparison of summary measures for the effectiveness of screening: the receiver characteristic curve (ROC) and the area under the ROC; and (3) to answer the question of which covariates effect which biomarkers and whether accounting for relevant covariates increases the prognostic value of biomarkers to levels that allow for application in the general population.

METHODS

In a representative cross-sectional health survey in northeast Germany with data collection from 1997 to 2001, 4310 men and women were asked for their recent alcohol consumption and smoking. Biomarkers were analyzed from blood samples. The effectiveness of screening of CDT, GGT, and MCV for high-risk drinking (men: >60 g/day, women: >40 g/day) was analyzed with PPV and ROC curve analysis.

RESULTS

For all three biomarkers, PPVs for high-risk drinking are very low (< 50%). There are some effects of covariates on screening effectiveness and on PPV, and knowledge of these covariates increases screening effectiveness, but no subgroup that had a combination of covariate levels and prevalence of high-risk drinking that led to a PPV > 50% could be found.

CONCLUSIONS

: Accounting for covariates in the screening procedure does not lead to a sufficient increase in PPV. Screening effectiveness of laboratory markers CDT, GGT, and MCV is insufficient for their application as screening tools for high-risk alcohol drinking in the general population. This was found using self-reported alcohol consumption as an imperfect gold standard, which is a limitation of the study, although self-reports are the standard instrument in comparable epidemiologic studies.

Chlamydia trachomatis infections in neonates and young children

In 1911, Lindner and colleagues identified intracytoplasmic inclusions in infants with a nongonococcal form of ophthalmia neonatorum called inclusion conjunctivitis of the newborn (ICN). Mothers of affected infants were found to have inclusions in their cervical epithelial cells, fathers of such infants had inclusions in their urethral cells, and the epidemiology of sexually transmitted chlamydial infections was revealed. Fifty years later, chlamydial isolation procedures were developed, and studies again demonstrated Chlamydia trachomatis as an etiology of ICN and the female birth canal as the reservoir. In the late 1970s, a report by Beem and Saxon described respiratory tract colonization and a distinct pneumonia syndrome in infected infants. Genital chlamydial infection is recognized as the world's most common sexually transmitted disease, with estimates of greater than 4 million new infections occurring annually in the United States. Although most C. trachomatis infections in men and women are asymptomatic, infection can lead to severe reproductive complications in women. The high prevalence in women of child-bearing age results in exposure of an estimated 100,000 neonates in the United States annually. Many of these infants develop conjunctivitis, pneumonia, or both in the first few months of life. Clinical features, diagnosis, treatment, and approaches to prevention of conjunctivitis and pneumonia in the newborn and young infant are reviewed here. Appropriate testing for chlamydial infection in a pediatric victim of sexual assault and the implications of identifying C. trachomatis in suspected cases of childhood sexual abuse also are reviewed.

Evaluation of Nucleic Acid Amplification Tests in the Absence of a Perfect Gold-Standard Test

During the past 10 years, medical diagnostic testing for sexually transmitted infections (STIs) has changed markedly as a result of the rapid expansion and marketing of nucleic acid amplification tests (NAATs). Among such new DNA/RNA-amplification techniques are the polymerase chain reaction (PCR), the ligase chain reaction (LCR), and the transcription-mediated amplification (TMA) tests. Regrettably, the test evaluation process undergone by these tests has not always been rigorous or scientifically sound. Here, we review the controversy surrounding the statistical evaluation of these NAATs. We also review some of the traditional and recent statistical methods developed to estimate test sensitivity and specificity parameters in the absence of reliable gold-standard tests. In particular, we review the traditional latent class modeling approach that requires the assumption of independence between diagnostic tests conditional on the true disease status, and the more recent procedures that relax the conditional independence assumption. Finally, we apply some of these statistical modeling techniques to real data to estimate the sensitivity and specificity of a NAAT for Chlamydia trachomatis. On the basis of the latent class modeling approach with a pessimistic prior for culture sensitivity, the NAAT specificity estimate was 97.6% and, on the basis of an optimistic prior, the specificity was 95.3%. Similarly, the sensitivity estimates ranged from 88.1% to 89.6%.

Evaluation of conventional and real-time PCR assays using two targets for confirmation of results of the COBAS AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae test for detection of Neisseria gonorrhoeae in clinical samples

Two conventional PCR-enzyme immunoassays (PCR-EIAs) and two real-time PCR assays (LightCycler system; Roche Diagnostics) were evaluated as confirmation assays with cppB and 16S rRNA genes as targets. Of 765 male and female genitourinary and nasopharyngeal specimens positive for Neisseria gonorrhoeae in the COBAS AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae PCR test (Roche Diagnostics), 229 (30%) were confirmed positive; 13 of these (5.7%) were lacking the cppB gene. Of the 534 samples (70%) that could not be confirmed, 81 (15%) showed a positive crossing point. However, melting curve analysis revealed an aberrant melting temperature in the LightCycler 16S rRNA assay; therefore, these samples were considered non-N. gonorrhoeae Neisseria species. Both of the 16S rRNA assays performed well, with positive predictive values of 99.1% and 100% for the PCR-EIAs and the real-time assays, respectively, and a negative predictive value of 99.8% for both. The cppB assays were compromised by the absence of the cppB gene in 5.7% of the N. gonorrhoeae-positive samples, resulting in negative predictive values of 96.8% and 97.6% for the PCR-EIAs and the real-time assays, respectively. Therefore, the 16S rRNA gene is preferable to the cppB gene as a target for confirmation assays. The melting curve analysis of the real-time assays provides useful additional information.

Comparison of COBAS AMPLICOR Neisseria gonorrhoeae PCR, including confirmation with N. gonorrhoeae-specific 16S rRNA PCR, with traditional culture

A total of 3,023 clinical specimens were tested for Neisseria gonorrhoeae by using COBAS AMPLICOR (CA) PCR and confirmation of positives by N. gonorrhoeae-specific 16S rRNA PCR. The sensitivity of CA plus 16S rRNA PCR was 98.8%, compared to 68.2% for culture. Confirmation of CA positives increased the positive predictive value from 54.8 to 96.6%.

Molecular genetic methods for diagnosis and characterisation of Chlamydia trachomatis and Neisseria gonorrhoeae: impact on epidemiological surveillance and interventions

One of the mainstays in the prevention of Chlamydia trachomatis and Neisseria gonorrhoeae infections is the availability of laboratory diagnostics with high sensitivity and specificity. Assays for diagnosis of C. trachomatis include cell culture and nucleic acid amplification tests (NAATs). The major target sequences for C. trachomatis diagnosis by NAATs are located at the cryptic plasmid and the major target used for characterisation is the omp1 gene. The gold standard for diagnosis of N. gonorrhoeae is culture. However, numerous NAATs for identification of N. gonorrhoeae and a number of molecular genetic methods for characterisation of N. gonorrhoeae have been developed. Probably no routine laboratory can attain as high sensitivity by culturing C. trachomatis or N. gonorrhoeae as by using NAATs. For that reason NAATs can be recommended for diagnosing C. trachomatis, but not as the only diagnostic assay for N. gonorrhoeae, due to lack of antibiotic susceptibility testing and specificity problems, most pronounced for pharyngeal and rectal samples. Genotyping of C. trachomatis or N. gonorrhoeae provides additional information for contact tracing. It is recommended for N. gonorrhoeae, at least in low prevalence geographic areas, but cannot today be recommended for C. trachomatis. This is due to the low genetic variability and hence the limited benefits for partner notification. However, genotyping of C. trachomatis may play an important role under special circumstances.

Genetic typing of the porin protein of Neisseria gonorrhoeae from clinical noncultured samples for strain characterization and identification of mixed gonococcal infections

Molecular methods that characterize the Neisseria gonorrhoeae porin protein Por are needed to study gonococcal pathogenesis in the natural host and to classify strains from direct clinical samples used with nucleic acid amplification-based tests. We have defined the capabilities of por variable region (VR) typing and determined suitable conditions to apply the method to direct clinical specimens. Nested PCR from spiked urine samples detected 1 to 10 copies of template DNA; freezing spiked whole urine greatly reduced the ability to amplify porB. In a laboratory model of mixed gonococcal infections, the por type of one strain could be determined in the presence of a 100-fold excess of another. por VR typing was used to examine clinical samples from women enrolled in studies conducted in Baltimore, Md., and Madagascar. por type was determined from 100% of paired cervical swab and wick samples from 20 culture-positive women from Baltimore; results for eight individuals (40%) suggested infection with more than one strain. In frozen urine samples from Madagascar, porB was amplified and typed from 60 of 126 samples from ligase chain reaction (LCR)-positive women and 3 samples from LCR-negative women. The por VR types of 13 samples (21%) suggested the presence of more than one gonococcal strain. Five por types, identified in >45% of women with typed samples, were common to both geographic areas. Molecular typing is an important adjunct to nucleic acid amplification-based diagnostics. Methods that utilize direct clinical samples and can identify mixed infections may contribute significantly to studies of host immunity, gonococcal epidemiology, and pathogenesis.

Comparison of nucleic acid amplification tests and culture techniques in the detection of Neisseria gonorrhoeae and Chlamydia trachomatis in victims of suspected child sexual abuse

STUDY OBJECTIVES

(1) To identify factors predictive for gonorrhea and chlamydia positivity by LCR testing based on history and physical findings encountered during the sexual abuse evaluations. (2) To compare Ligase Chain Reaction (LCR), Polymerase Chain Reaction (PCR), and culture methods in the detection of chlamydia and gonorrhea infection among prepubertal and adolescent girls referred for sexual abuse evaluations.

DESIGN

Prevalence odds ratios and logistic regression analysis were used to identify factors among patients' physical symptoms and signs, history of sexual activity, and abuse characteristics that were associated with positive test results for gonorrhea and chlamydia. The Kappa statistic was used to perform pairwise comparisons of LCR, PCR, and culture identification of gonorrhea and chlamydia infection.

SETTING

A specialized sexual abuse clinic in San Antonio, Texas.

PARTICIPANTS

A consecutive sample of 229 girls between the ages of 6 and 20 who reported, or had indicators of, abusive genital-genital or genital-anal contact.

MAIN OUTCOME MEASURES

Patients' history and physical findings predicting positive test results for gonorrhea and chlamydia infection; and relative sensitivity of testing sites (vaginal swab and urine) and methodologies (LCR, PCR, and culture) in identifying gonorrhea and chlamydia infection.

RESULTS

(1) Gonorrhea infection: 3.2% of subjects were positive for gonorrhea by LCR at one or more sites; 2.4% had positive gonorrhea cultures. There was excellent agreement between vaginal swab LCR and PCR; agreement between urine samples was limited by the small number of positive tests. The sole factor that predicted gonorrhea positivity was increased number of white blood cells seen on wet mount. (2) Chlamydia infection: 11.1% of subjects were positive for chlamydia by at least one LCR test; only 0.8% had positive chlamydia cultures. Both urine and vaginal swab testing showed good agreement between PCR and LCR but not between culture and either of the newer methodologies. Factors that predicted chlamydia positivity were: patient history of consensual sexual contact, patient history of vaginal discharge, and the presence of concerning or definitive findings of genital trauma.

CONCLUSIONS

While LCR, PCR, and culture techniques appeared comparable for detecting gonorrhea, LCR techniques detected significantly more patients with chlamydia infection when compared with the culture technique. PCR was comparable to LCR in detecting chlamydia infection. The LCR vaginal swab detected more patients with chlamydia and gonorrhea than the LCR urine sample. Risk factors for chlamydia and gonorrhea infection were present in most, but not all, of the children with positive LCR findings. LCR and PCR appear to detect more chlamydial and gonorrheal infections than do cultures.

Comparison of the APTIMA CT and GC assays with the APTIMA combo 2 assay, the Abbott LCx assay, and direct fluorescent-antibody and culture assays for detection of Chlamydia trachomatis and Neisseria gonorrhoeae

The Gen-Probe APTIMA Combo 2 (AC2) is a Food and Drug Administration-cleared nucleic acid amplification test (NAAT) for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae from urine and urogenital swab specimens. The Centers for Disease Control and Prevention have recommended confirmation of positive NAAT results in low-prevalence populations. APTIMA CT (ACT) and APTIMA GC (AGC) are two discrete NAATs for C. trachomatis and N. gonorrhoeae detection that are suitable for confirming AC2-positive results because they target different nucleic acid sequences. Our objective was to determine if ACT and AGC could be used as confirmatory tests for AC2 and to correlate the APTIMA assays with culture, direct fluorescent-antibody (DFA), and LCx CT and GC assays. Urine and swab specimens (1,304) were initially tested with either culture, DFA, or LCx, followed by AC2. A subset (675) was then tested with ACT and AGC. There was absolute concordance between ACT-AGC and AC2. LCx did not detect 1 of 14 AC2-ACT- and 1 of 6 AC2-AGC-positive urine samples, and it yielded one C. trachomatis- and one N. gonorrhoeae-positive swab result that were not detected by AC2 and ACT-AGC. Culture failed to detect 5 of 20 AC2-ACT and 3 of 4 AC2-AGC positives, and DFA missed 4 of 4 AC2-ACT positives. Thus, ACT and AGC relative sensitivity compared to that of AC2 was 100%. All APTIMA assays detected more confirmed positive results than culture, DFA, and LCx. The performance of APTIMA assays was not altered by the use of various swab types and by long-term storage of specimens. All APTIMA assays are highly sensitive and rapid. ACT and AGC can be recommended for confirmation of positive results from other NAATs, such as AC2 and LCx.

Evaluation of real time polymerase chain reaction assays for confirmation of Neisseria gonorrhoeae in clinical samples tested positive in the Roche Cobas Amplicor assay

OBJECTIVE

Development of a rapid, sensitive, and accurate assay for confirmation of Neisseria gonorrhoeae in clinical samples.

METHOD

Two real time polymerase chain reaction (PCR) assays, developed on the LightCycler for amplification of the N gonorrhoeae cppB gene, were utilised for confirmation of this bacterial pathogen in samples positive by the Roche Cobas Amplicor assay. Performance characteristics of the two assays were compared with other commercial nucleic acid amplification assays, including the Abbott LCx and Roche 16S rRNA tests.

RESULTS

All related Neisseria as well as other bacterial species tested negative by both cppB gene based assays, whereas 120 N gonorrhoeae clinical isolates from various geographical regions gave in positive results. Both assays had a sensitivity of one copy per reaction. 122 clinical samples positive and another 50 samples negative for N gonorrhoeae by Roche Cobas Amplicor were selected from a specimen pool of more than 3000 women tested previously. Overall, 73 of 122 (59.8%) samples were confirmed as positive. The two real time assays had sensitivities of 99% and 100% and specificities of 98% and 100%, respectively. The 16S and LCx assays produced similar results to the real time assays, indicating a similar sensitivity to and specificity of both real time assays.

CONCLUSION

The data from this study highlight the need to confirm N gonorrhoeae positive Cobas Amplicor PCR results as an important part of the testing algorithm of all diagnostic laboratories utilising this assay.

False-positive gonorrhea test results with a nucleic acid amplification test: the impact of low prevalence on positive predictive value

Five false-positive gonorrhea test results from a private laboratory using a nucleic acid amplification test led to an investigation by the Hawaii State Department of Health. No unexplained increase or variation in the laboratory's positive gonorrhea test results was detected. The proportion of positive gonorrhea test results among tests performed in the population was 1.06%. The calculated positive predictive value (PPV) of the test in this setting was 60%. Documentation of sexual histories was lacking for all cases. It is imperative to obtain a sexual history for both assessing sexually transmitted disease (STD) risk and interpreting STD test results. The possibility that positive test results may be false should be considered when patients have unanticipated positive test results. Clinicians who perform STD screening tests should know the approximate prevalence of STDs in the population being screened and have a conceptual understanding of PPV and the impact of low prevalence on screening tests with imperfect specificity.

Acute urethritis caused by Neisseria meningitidis

A 48-year-old heterosexual Japanese man visited the outpatient clinic of Nagoya Urology Hospital, complaining of burning pain at voiding and pus discharge from the urethral orifice. These symptoms appeared the day following oral-genital contact (fellatio) with a commercial sex worker. On the basis of the presumptive clinical diagnosis of gonorrhea because of the microscopic detection of diplococci in the urethral discharge, he was treated with levofloxacin (300 mg per day) for 7 days. His symptoms responded quickly and urinalysis taken 7 days later was normal. Microbiological examinations isolated Neisseria meningitidis in the urethral discharge by culture with the use of enzymatic profiles. Further prevalence of sexually transmitted diseases (STD) through oral-genital contact would lead to an increase in meningococcal urethritis.

Confirmation by 16S rRNA PCR of the COBAS AMPLICOR CT/NG test for diagnosis of Neisseria gonorrhoeae infection in a low-prevalence population

The COBAS AMPLICOR CT/NG test is widely used for the diagnosis of Neisseria gonorrhoeae infection using genital swabs or urine samples. Although highly specific, cross-reactivity occurs with some nonpathogenic strains of Neisseria and Lactobacillus species. In low-prevalence populations, even highly specific assays may require confirmatory testing of positive results. We assessed the positive predictive value (PPV) of this test in a low-prevalence (0.5%) setting. Genital and urine specimens testing positive using the COBAS AMPLICOR NG test were retested using an investigational 16S rRNA PCR assay. Additionally, 737 specimens were tested in parallel by both culture and the above PCR protocol. Of 9,772 specimens tested in-house, 168 were positive by the AMPLICOR test; in addition, 62 AMPLICOR-positive specimens were referred to our laboratory for confirmatory testing, yielding 230 positive specimens. Of these, 72 were confirmed positive by 16S rRNA PCR, yielding a specificity of 98.7% and a PPV of 31.3%. Specificity was similar for all specimen types, whereas PPV varied with prevalence: specimens from males, females, urine specimens, and genital swabs had PPVs of 70.8, 13.3, 51.9, and 20.1%, respectively. The PPV was higher when the initial AMPLICOR optical density (OD) was > or =3.5 versus initial and repeat OD readings in an equivocal zone of > or =0.2 to <3.5 (65.1 versus 10.1%; P < 0.001). On repeat testing of specimens with ODs in the equivocal zone, 54 gave ODs of > or =0.2 and <2.0, 35 gave ODs of > or =2.0 and <3.5, and 12 gave ODs of > or =3.5, with 3.7, 20, and 33.3% confirmed positive, respectively (P = 0.004). Comparing PCR to culture as the "gold standard," specificity increased from 96.8 to 99.9% when 16S rRNA PCR was performed on specimens positive by the COBAS AMPLICOR NG test. Confirmatory testing with a more specific method such as 16S rRNA PCR should be considered in low-prevalence populations, especially for specimens with an OD in the equivocal zone.