Ligase chain reaction for detection of Neisseria gonorrhoeae in urogenital swabs

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.

Gonorrhoea diagnostics: An update

Diagnosis of gonorrhoea is an ongoing challenge. The organism is fastidious requiring meticulous collection and transport for successful cultivation. Asymptomatic infections are common which go undetected by conventional methods thereby leading to continued transmission and the risk of complications. The nucleic acid amplification tests, now increasingly used in developed countries, offer improved sensitivity compared to bacterial culture. However, these continue to suffer sequence related problems leading to false positive and false negative results. Further, these cannot be used for generation of data on antibiotic susceptibility because genetic markers of antibiotic resistance to recommended therapies have not been fully characterised. They are unaffordable in a setting like ours where reliance is placed on syndromic approach for sexually transmitted infection (STI) management. The use of syndromic approach has resulted in a considerable decline in the number of Neisseria gonorrhoeae isolates that have been cultured for diagnostic purposes. Many laboratories formerly doing so are no longer performing culture for gonococci, and the basic skills have been lost. There is a need to not only revive this skill but also adopt newer technologies that can aid in accurate diagnosis in a cost-effective manner. There is room for innovation that can facilitate the development of a point-of-care test for this bacterial STI.

Cost-Effectiveness of Screening Strategies for Gonorrhea Among Females in Private Sector Care

OBJECTIVE

To identify the optimal screening algorithm for gonorrhea infection among females in private sector care, using cost-effectiveness analysis.

METHODS

We compared 6 strategies using decision analysis for urine nucleic acid amplification testing for gonorrhea testing in a theoretical cohort of 10,000 females aged 15-35 years: 1) screen women aged younger than 25 years; 2) screen women aged younger than 30 years; 3) screen women aged younger than 25 years who report any risk (pregnant, drug use, new sexual partner < 30 days); 4) screen women aged younger than 30 years who report any risk; 5) screen women aged younger than 25 years or those who report any risk; and 6) screen women aged younger than 30 years or those who report any risk. Infection prevalence and sensitivity and specificity were by direct observation from a retrospective cohort of females attending the Baltimore City Sexually Transmitted Disease Clinics between 1999 and 2002. The main outcome measures were untreated gonorrhea cases and their sequelae in women, transmission to a male partner, congenital outcomes, and cost to prevent a case.

RESULTS

Prevalence of gonorrhea was 3.0%. Not screening would result in 300 untreated cases. Not screening was cost-saving over all screening strategies. Strategy 6 resulted in the fewest cases of untreated infection (82), although Strategy 3 was the most cost-effective of the screening strategies. Univariate sensitivity analysis identified a threshold of 4.75% gonorrhea prevalence, more than which Strategy 3 became cost-saving over not screening.

CONCLUSION

Screening is recommended for females aged younger than 25 years with specific risks in populations with a gonorrhea prevalence of 4.75% or greater.

LEVEL OF EVIDENCE

II-2.

Nucleic acid amplification testing for Neisseria gonorrhoeae: an ongoing challenge

Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review.

Specific and sensitive detection of Neisseria gonorrhoeae in clinical specimens by real-time PCR

Early diagnosis of Neisseria gonorrhoeae infections is important with regard to patients' health and infectivity. We report the development of a specific and sensitive TaqMan assay for the detection of N. gonorrhoeae in clinical samples. The target sequence is a 76-bp fragment of the 5' untranslated region of the opa genes that encode opacity proteins. A panel of 448 well-defined N. gonorrhoeae isolates was used to evaluate and optimize the assay. The method employs two minor-groove binding probes, one of them recognizing a newly identified sequence in the opa genes. Testing a large panel of related and unrelated microorganisms revealed that other Neisseria strains and other microorganisms tested negative in the opa test. With a lower detection limit of one genome per reaction, the opa test appeared more sensitive than both the COBAS AMPLICOR (Roche Diagnostics Nederland BV, Almere, The Netherlands) and a LightCycler 16S rRNA test. Analysis of a panel of 122 COBAS AMPLICOR-positive samples revealed that 68% were negative in both the 16S rRNA test and the opa assay (confirming that the COBAS AMPLICOR test produces false positives), while 30% were positive in both assays. Three samples were opa positive and 16S rRNA negative, which may be due to the higher sensitivity of the opa assay. We conclude that the opa gene-based real-time amplification assay offers a sensitive, specific, semiquantitative, and reliable assay suitable for the detection of N. gonorrhoeae in clinical specimens and/or for confirmation of less specific tests.

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.

Sexually Transmitted Disease/HIV Transmission Risk Behaviors and Sexually Transmitted Disease Prevalence Among HIV-Positive Men Receiving Continuing Care

OBJECTIVE

HIV primary care clinics offer an environment in which to deliver prevention messages and to conduct sexually transmitted disease (STD) screening. Determination of the prevalence and factors associated with risk-taking behaviors among HIV clinic attendees is needed.

GOAL

The goal of this study was to describe risk behaviors and STD prevalence in males receiving HIV primary care.

STUDY

Participants underwent an interviewer-administered survey and STD testing during this cross-sectional study.

RESULTS

Over two thirds of study participants reported sexual activity within the prior 6 months of which 6% were infected with gonorrhea or chlamydia. Men performing insertive rectal sex were 5 times less likely to use condoms when the partner was HIV-positive (odds ratio [OR], 5.14; 95% confidence interval [CI], 1.90-13.91), whereas patients with higher CD4 counts were more likely to engage in unprotected receptive rectal sex (OR, 1.20; 95% CI, 1.02-1.42).

CONCLUSION

HIV primary care clinics provide access to patients in need of HIV prevention intervention and are appropriate sites for these activities.

The effect of urine testing in evaluations of the sensitivity of the Gen-Probe Aptima Combo 2 assay on endocervical swabs for Chlamydia trachomatis and neisseria gonorrhoeae: the infected patient standard reduces sensitivity of single site evaluation

BACKGROUND

The Gen-Probe APTIMA Combo 2 (AC2) assay is a second-generation transcription-mediated amplification assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG).

GOAL

The goal of this study was to evaluate AC2 performance of endocervical (cx) swabs for the detection of CT and NG using either a specimen or an infected patient standard.

STUDY DESIGN

In a multicenter clinical study, we compared AC2 with Abbott's ligase chain reaction (LCR) and Roche's polymerase chain reaction (PCR; Amplicor or COBAS) for CT, and we compared AC2 with Abbott's LCR and culture for NG. A total of 1569 females were enrolled in the study; we collected cx and first-catch urine (FCU) specimens.

RESULTS

CT prevalence was 13.3% for cx specimens and 13.7% for FCU specimens. NG prevalence was 8.7% and 7.9% for cx and FCU specimens, respectively. When based only on cx specimens, AC2, LCR, and PCR sensitivities for CT were 99.4%, 95.6%, and 95.6%, respectively. However, cx sensitivity for CT was reduced to 92.1%, 86.6%, and 87.1% for each respective assay when based on both cx and FCU specimen results (infected patient standard). NG sensitivities for AC2, LCR, and culture based solely on cx specimen results were 99.2%, 96.1%, and 85.9%, respectively. Based on infected patient standard, the sensitivities of each respective assay were 98.5%, 93.9%, and 84.0%.

CONCLUSIONS

The infected patient standard reduces the sensitivity of the endocervical evaluation because some infected patients are positive only with FCU. The reduction in sensitivity is greater when testing for CT. Specificities improved slightly, because some unique cx positives, initially classified as false-positive were confirmed by a positive FCU result. Sensitivity of AC2 was higher than LCR, PCR, and culture. Specificity was slightly lower, but discrepant analysis (using alternate TMA targets) of apparent AC2 false-positives showed that 75% to 80% were true-positives.

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.

Duration of persistence of gonococcal DNA detected by ligase chain reaction in men and women following recommended therapy for uncomplicated gonorrhea

Neisseria gonorrhoeae infection remains relatively common in the United States, representing a public health challenge. Ligase chain reaction (LCR) is both highly sensitive and specific for the detection of N. gonorrhoeae in urine and patient-obtained vaginal swab specimens. Because of the LCR test's exquisite sensitivity, it may potentially detect DNA from nonviable organisms following effective therapy, leading to false-positive test results and unnecessary additional treatment. The purpose of the present study was to determine the duration that gonococcal DNA is detectable by LCR following therapy for uncomplicated gonococcal infection. One hundred thirty men and women between the ages of 16 and 50 years presenting to a sexually transmitted disease clinic with urogenital gonorrhea were enrolled. After the standard history was taken and a genital examination was done, the patients were asked to submit either a urine specimen (men) or a urine specimen plus a self-obtained vaginal swab specimen (women) for N. gonorrhoeae testing by LCR at the initial visit and each day during the study period. At enrollment, patients were treated with single doses of ofloxacin, cefixime, or ceftriaxone. The median time to a negative urine LCR test result was 1 day for the men (mean, 1.6 +/- 0.14 days) and 2 days for the women (mean, 1.7 +/- 0.19 days). Among the women the clearance time was significantly longer for vaginal specimens (mean, 2.8 +/- 0.30 days) than for urine specimens (mean, 1.7 +/- 0.11 days). Irrespective of patient gender and specimen type, gonococcal DNA can be expected to be absent from urogenital specimens within 2 weeks following successful therapy.

The Use of Urine and Self-obtained Vaginal Swabs for the Diagnosis of Sexually Transmitted Diseases

Studies have reported that self-collected specimens, such as urine or vaginal swabs, can be successfully used to diagnose sexually transmitted infections when they are used with nucleic acid amplification assays. This eliminates the necessity for a clinician-performed pelvic examination for women, or a urethral swab for men, for sample collection. These nucleic acid amplification assays used with self-collected specimens are highly sensitive and specific, and their use may be extended to broad nonclinic screening venues, where their use can augment public health programs designed to control the epidemic of sexually transmitted diseases.

Comparison of Digene hybrid capture 2 and conventional culture for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in cervical specimens

Digene's Hybrid Capture 2 (HC2) CT/GC, CT-ID, and GC-ID DNA tests were evaluated by comparison to traditional culture methods for detecting Chlamydia trachomatis and Neisseria gonorrhoeae infections in 669 cervical specimens from high-risk female populations attending two sexually transmitted disease clinics. For detection of either or both infections, the HC2 CT/GC test algorithm had 93.8% sensitivity and 95.9% specificity compared to those of culture. After resolution of discrepant results by direct fluorescent-antibody (DFA) staining or PCR assay, the relative sensitivity and specificity of the HC2 CT/GC test algorithm increased to 94.8 and 99.8%, while the values for culture were 83.6% (McNemar's P value, 0.0062) and 100%, respectively. For detection of the individual pathogens, the relative sensitivities for the HC2 CT-ID and GC-ID tests were 97.2 and 92.2% and the specificities were greater than 99% compared to culture adjucated by DFA staining and PCR. Test performance varied at the two clinics: the HC2 CT/GC algorithm, CT-ID, and GC-ID tests had significantly higher sensitivities (McNemar's P value, <0.05) than that of culture for the population at one clinic as well as for the combined populations. At the other clinic, the HC2 tests performed as well as culture.

Use of ligase chain reaction for laboratory identification of Chlamydia trachomatis and Neisseria gonorrhoeae in adolescent women

STUDY OBJECTIVE

To compare the ligase chain reaction (LCR) with culture for the detection of Neisseria gonorrhoeae (GC) and with culture and direct fluorescent antibody (DFA) for identification of Chlamydia trachomatis (CT) in cervical specimens from adolescent women.

DESIGN

A prospective study of test performance.

SETTING

Two urban, hospital-based adolescent clinics.

PARTICIPANTS

Adolescent women aged 12-22 yr undergoing pelvic examination for routine sexually transmitted disease (STD) screening or symptoms suggestive of an STD.

MAIN OUTCOME MEASURES

LCR results were considered to be true positives if confirmed by culture and/or DFA (CT only). Discrepant LCR results were confirmed by testing an alternative locus.

RESULTS

With 538 subjects, LCR for CT had a sensitivity of 98.4% (61/62) and specificity of 96.4% (459/476) prior to resolution and a sensitivity of 98.6% (70/71) and specificity of 99.6% (459/461) after resolution. With 1225 subjects, LCR for GC had a sensitivity of 90.0% (54/60) and specificity of 99.4% (1158/1165) prior to resolution and a sensitivity of 90.6% (58/64) and specificity of 100% (1158/1158) after resolution. CT culture alone identified 80% of the true positives and DFA alone only identified 72%. GC culture alone identified 94% of the true positives.

CONCLUSIONS

LCR is an extremely sensitive and specific rapid test, utilizing a single swab and convenient room-temperature storage and transport of specimens. LCR testing of cervical specimens for CT in adolescent women is a better test for detecting CT infection than culture or DFA. LCR testing for cervical GC infection may provide an advantage over culture in circumstances in which optimal transport conditions and viability of the organism cannot be assured.

Comparison of Digene hybrid capture 2 and conventional culture for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in cervical specimens

Digene's Hybrid Capture 2 (HC2) CT/GC, CT-ID, and GC-ID DNA tests were evaluated by comparison to traditional culture methods for detecting Chlamydia trachomatis and Neisseria gonorrhoeae infections in 669 cervical specimens from high-risk female populations attending two sexually transmitted disease clinics. For detection of either or both infections, the HC2 CT/GC test algorithm had 93.8% sensitivity and 95.9% specificity compared to those of culture. After resolution of discrepant results by direct fluorescent-antibody (DFA) staining or PCR assay, the relative sensitivity and specificity of the HC2 CT/GC test algorithm increased to 94.8 and 99.8%, while the values for culture were 83.6% (McNemar's P value, 0.0062) and 100%, respectively. For detection of the individual pathogens, the relative sensitivities for the HC2 CT-ID and GC-ID tests were 97.2 and 92.2% and the specificities were greater than 99% compared to culture adjucated by DFA staining and PCR. Test performance varied at the two clinics: the HC2 CT/GC algorithm, CT-ID, and GC-ID tests had significantly higher sensitivities (McNemar's P value, <0.05) than that of culture for the population at one clinic as well as for the combined populations. At the other clinic, the HC2 tests performed as well as culture.

Increased sensitivity of DNA amplification testing for the detection of pharyngeal gonorrhea in men who have sex with men

We compared ligase chain reaction (LCR) assay with standard culture for the detection of pharyngeal Neisseria gonorrhoeae infection in men who have sex with men (MSM) presenting at a sexually transmitted diseases clinic in San Francisco. Pharyngeal specimens were obtained from 200 MSM who reported performing fellatio during the previous 2 weeks. Confirmatory testing of discrepant specimens was conducted using N. gonorrhoeae pilin proteins. Prevalence of pharyngeal N. gonorrhoeae was 6% by culture or 11% by LCR. The sensitivity and specificity of LCR were 94.7% and 97.8%, respectively, compared with values of 47.4% and 100% for culture. Prevalence of pharyngeal N. gonorrhoeae infection, as determined by DNA amplification testing, was higher than that suggested by traditional culture. Results support the use of DNA amplification testing in the oropharynx. The high prevalence of pharyngeal N. gonorrhoeae infection among MSM suggests that routine screening should be considered in efforts to reduce the burden of gonorrhea in this population.

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

The COBAS AMPLICOR CT/NG test for Neisseria gonorrhoeae cross-reacts with certain strains of nonpathogenic Neisseria species. In some strains, the target sequence is identical to that of N. gonorrhoeae, whereas other strains have a small number of mismatches within the regions recognized by the primers or probe used in the COBAS AMPLICOR NG test. These cross-reactive strains are occasionally present in urogenital specimens, causing false-positive results in the COBAS AMPLICOR NG test. Analysis of the data generated in a large multicenter clinical trial showed that 2.9% of the specimens gave signals between A(660)s of 0.2 and 3.5 but that one-half of these equivocal specimens did not contain N. gonorrhoeae. Most of these equivocal specimens were correctly classified as true positive or true negative by retesting in duplicate and defining a PCR-positive result as two of three results with an A(660) of > or =2.0. If specimens had been classified as positive or negative based on a single test result using a cutoff of an A(660) of 0.2, specificity would have ranged from 96.2 to 98.9% depending on specimen type, sex, and presence of symptoms. By employing the equivocal zone-retesting algorithm, specificity increased to 98.6 to 99.9% with little effect (0.1 to 4.9% decrease) on sensitivity in most specimen types, enabling the test to achieve a positive predictive value of at least 90% in populations with a prevalence of 4% or higher. In lower-prevalence populations, the test could be used to screen for presumptive infections that would have to be confirmed by an independent test.

Evaluation of the Roche Neisseria gonorrhoeae 16S rRNA PCR for confirmation of AMPLICOR PCR-positive samples and comparison of its diagnostic performance according to storage conditions and preparation of endocervical specimens

The AMPLICOR PCR was used to detect Neisseria gonorrhoeae in endocervical specimens. A 16S rRNA PCR performed on N. gonorrhoeae-positive samples showed sensitivities of 73.2, 64.3, and 94.4% for samples treated directly with AMPLICOR lysis buffer, samples suspended in 2-sucrose phosphate, and samples suspended in diluted phosphate-buffered saline, respectively.

Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by enzyme immunoassay, culture, and three nucleic acid amplification tests

The purpose of this study was to evaluate and compare three commercially available nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis. Roche PCR and Becton Dickinson strand displacement amplification (SDA) were performed on 733 endocervical swab specimens from commercial sex workers. Abbott ligase chain reaction (LCR) was performed on a subset of 396 samples. Endocervical specimens from all women were also tested by culture for N. gonorrhoeae and by Syva MicroTrak enzyme immunoassay (EIA) for C. trachomatis. A positive N. gonorrhoeae result was defined as a positive result by culture or by two NAATs, and a positive C. trachomatis result was defined as a positive result by two tests. According to these definitions, the sensitivities and specificities for the subsample of 396 specimens of N. gonorrhoeae culture, PCR, SDA, and LCR were 69.8, 95.2, 88.9, and 88.9% and 100, 99.4, 100, and 99.1%, respectively; the sensitivities and specificities of C. trachomatis EIA, PCR, SDA, and LCR were 42.0, 98.0, 94.0, and 90.0% and 100, 98.0, 100, and 98.6%, respectively. The performance characteristics of N. gonorrhoeae culture, PCR, and SDA and C. trachomatis EIA, PCR, and SDA for all 733 specimens were defined without inclusion of LCR results and by discrepant analysis after resolution of discordant N. gonorrhoeae PCR results and of discordant C. trachomatis EIA and PCR results by LCR testing. The sensitivities of N. gonorrhoeae culture, PCR, and SDA before and after LCR resolution were 67.8, 95.7, and 93.9% and 65, 95.8, and 90.0%, respectively. The sensitivities of C. trachomatis EIA, PCR, and SDA decreased from 39.4, 100, and 100% to 38.7, 98.7, and 94.7%, respectively. All three NAATs proved to be superior to N. gonorrhoeae culture and to C. trachomatis EIA. The accuracies of the different NAATs were quite similar. SDA was the only amplification assay with 100% specificity for detection of both N. gonorrhoeae and C. trachomatis in endocervical specimens.

Molecular diagnostics of infectious diseases: state of the technology

In this review, the basic technologies and procedures currently used in clinical laboratories performing molecular diagnostics are described. Special emphasis on specimen processing has been made since it is one of the most challenging steps involved in molecular testing. Representative examples are given for each type of technology, especially tests that are currently available in the market. The types of hybridization-based and amplification-based procedures are detailed. Finally, current problems and future developments are discussed.

Comparison of the urine-based ligase chain reaction test to culture for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in pediatric sexual abuse victims

BACKGROUND

The urine-based ligase chain reaction (LCR) assay for Chlamydia trachomatis and Neisseria gonorrhoeae is an attractive alternative to culture because of the relative ease with which specimens may be collected, transported and processed. In addition LCR offers superior sensitivity while maintaining high specificity when compared with culture in various studies of adolescents and adults. A study comparing LCR to culture has not been published concerning children.

METHODS

We conducted a prospective, comparison trial of the urine-based LCR test for Chlamydia trachomatis and Neisseria gonorrhoeae as compared with culture among children at a specialized referral center for evaluation for alleged sexual assault. Of the 1,010 children presenting to the center during the study period, 164 met the study requirements for risk of a sexually transmissible disease and collection of both culture and urine LCR specimens.

RESULTS

Eight specimens tested positive by both methods for C. trachomatis. Another 10 specimens tested positive for C. trachomatis by LCR but were negative by culture. No patient with a negative LCR for C. trachomatis had a positive culture. For N. gonorrhoeae 2 specimens tested positive by both methods, and 3 specimens tested positive by LCR but negative by culture. No patient with a negative LCR for N. gonorrhoeae had a positive culture.

CONCLUSIONS

The low prevalence of disease in the study population precluded statistical analysis. LCR may prove to be as specific and more sensitive than culture for the detection of C. trachomatis and N. gonorrhoeae in children. Further studies are needed.

Multicenter evaluation of AMPLICOR and automated COBAS AMPLICOR CT/NG tests for Neisseria gonorrhoeae

The fully automated COBAS AMPLICOR CT/NG and semiautomated AMPLICOR CT/NG tests were evaluated in a multicenter trial for their ability to detect Neisseria gonorrhoeae infections. Test performance compared to that of culturing was evaluated for 2,192 matched endocervical swab and urine specimens obtained from women and for 1, 981 matched urethral swab and urine specimens obtained from men. Culture-negative, PCR-positive specimens that tested positive in a confirmatory PCR test for an alternative target sequence within the N. gonorrhoeae 16S rRNA gene were considered to be true positives. The overall prevalences of gonorrhea were 6.6% in women and 20.1% in men. The COBAS AMPLICOR and AMPLICOR formats yielded concordant results for 98.8% of the specimens and exhibited virtually identical sensitivities and specificities. The results that follow are for the COBAS AMPLICOR format. With the infected patient as the reference standard, the resolved sensitivities of PCR were 92.4% for endocervical swab specimens and 64.8% for female urine specimens. There were no significant differences in these rates between women with and without symptoms. Among symptomatic men, COBAS AMPLICOR sensitivities were 94.1% for urine and 98.1% for urethral swabs; for asymptomatic men, the results were 42.3 and 73.1%, respectively. In comparison, the sensitivities of culturing were 84.8% for endocervical specimens, 92.7% for symptomatic male urethral specimens, and only 46.2% for urethral specimens obtained from asymptomatic men. When PCR results were analyzed as if only a single test had been performed on a single specimen type, the resolved sensitivity was always higher. The resolved specificities of PCR were 99.5% for endocervical swab specimens, 99.8% for female urine specimens, 98.9% for male urethral swab specimens, and 99.9% for male urine specimens. The internal control revealed that 2.1% of specimens were inhibitory when initially tested. Nevertheless, valid results were obtained for 99.2% of specimens because 60.0% of the inhibitory specimens were not inhibitory when a second aliquot was tested. The COBAS AMPLICOR CT/NG test for N. gonorrhoeae exhibited high sensitivity and specificity with urethral swab and urine specimens from men and endocervical swab specimens from women and thus is well suited for diagnosing and screening for N. gonorrhoeae infection.

Opportunistic urine ligase chain reaction screening for sexually transmitted diseases in adolescents seeking care in an urban emergency department

STUDY OBJECTIVE

Neisseria gonorrhoeae and Chlamydia trachomatis are the most common bacterial sexually transmitted diseases (STDs) in sexually active youth and many infections are asymptomatic or unrecognized. This study used ligase chain reaction assays for determination of prevalence of gonococcal and chlamydial infections in adolescents seeking care at an urban emergency department.

METHODS

An unlinked prevalence study was performed with ligase chain reaction tests on voided urine specimens from a convenience sample of adolescents 14 years or older who sought care at the Children's Hospital of Alabama ED. Demographic data and data on care provided in the ED were determined from retrospective chart review of those patients whose urine specimens were tested.

RESULTS

Of 282 urine specimens screened, 13.5% (38) yielded positive findings on ligase chain reaction testing for either or both pathogens (20 [7%] positive for N gonorrhoeae, 23 [8%] positive for C trachomatis). In the context of acute care, gonorrhea or chlamydial infection was diagnosed in 5 (1.8%). STD prevalence did not vary significantly by age. Only 39% (15/38) of patients with infections detected by ligase chain reaction testing received potentially effective antibiotics as a result of their urgent care evaluation.

CONCLUSION

Many adolescents use the ED for nonurgent care and unsuspected STDs are often missed. Urine ligase chain reaction testing is a sensitive, noninvasive means of detecting STDs by which unsuspected adolescent STD cases can be detected in an ED setting.

Multicenter evaluation of the AMPLICOR and automated COBAS AMPLICOR CT/NG tests for detection of Chlamydia trachomatis

The fully automated COBAS AMPLICOR CT/NG and semiautomated AMPLICOR CT/NG tests were evaluated in a multicenter trial for the ability to detect Chlamydia trachomatis infections. Test performance compared to that of culture was evaluated for 2,236 matched endocervical swab and urine specimens obtained from women and for 1,940 matched urethral swab and urine specimens obtained from men. Culture-negative, PCR-positive specimens that tested positive in a direct fluorescent-antibody test or in a confirmatory PCR test for an alternative target sequence were resolved as true positives. The overall prevalences of chlamydia were 2.4% in women and 7.2% in men. The COBAS AMPLICOR and AMPLICOR formats yielded concordant results for 98.1% of the specimens. With the infected patient as the reference standard, the resolved sensitivities of COBAS AMPLICOR were 89.7% for endocervical swab specimens, 89.2% for female urine specimens, 88.6% for male urethral swab specimens, and 90.3% for male urine specimens. When results were analyzed as if only a single test had been performed on a single specimen type, the resolved sensitivity was always higher. The resolved specificities of PCR were 99.4% for endocervical swab specimens, 99.0% for female urine specimens, 98.7% for male urethral swab specimens, and 98.4% for male urine specimens. The internal control revealed that 2.4% of the specimens were inhibitory when initially tested. Nevertheless, valid results were obtained for 98.6% of the specimens because 59.1% of the inhibitory specimens were not inhibitory when a second aliquot was tested. The COBAS AMPLICOR and AMPLICOR CT/NG tests for C. trachomatis exhibited equally high sensitivity and specificity with both urogenital swab and urine specimens and thus are well suited for screening for C. trachomatis infection.

Behavioral and biologic evidence of persistent high-risk behavior in an HIV primary care population

OBJECTIVE

To define the prevalence of gonorrhea, chlamydial infection, and high-risk sexual behavior in an HIV primary care clinic.

DESIGN

Subjects enrolling in this cross-sectional study answered a brief interviewer-administered questionnaire and provided a urine sample for gonorrhea and chlamydia testing.

SETTING

A large urban HIV primary care clinic.

PARTICIPANTS

HIV-infected patients presenting for a scheduled medical visit from June 1997 to April 1998.

MAIN OUTCOME MEASURES

Prevalence of self-reported high-risk sexual behavior and gonorrhea and chlamydial infection.

RESULTS

Of 691 patients consenting to the study over a 10-month period, 58% reported sexual activity in the past 90 days, 7.4% reported multiple sexual partners in the past month, and 34.6% did not use a condom at last sexual encounter. Overall, 4.6% reported a history of either gonorrhea or a chlamydial infection in the past year. Of 637 giving a urine sample for testing, the prevalence of chlamydial infection was 2.4%; the prevalence of gonorrhea was 1.6%. Overall, 7.5% of those screened had either current or recent (within 1 year) gonorrhea or chlamydial infection. Current or recent gonorrhea or chlamydial infection was not associated with age, gender, HIV transmission risk, CD4 cell count, HIV viral load, symptoms, or self-reported risk behavior.

CONCLUSION

High-risk sexual behavior and unrecognized sexually transmitted diseases (STD) are common among HIV-infected persons followed in primary medical care. Enhanced detection of treatable STD among this population coupled with improved risk-reduction counselling may be important clinical practice measures that can curb the spread of HIV.

Using a combination of reference tests to assess the accuracy of a new diagnostic test

Often the accuracy of a new diagnostic test must be assessed when a perfect gold standard does not exist. Use of an imperfect reference test biases accuracy estimates of the new test. This paper reviews existing approaches to this problem including discrepant resolution and latent class analysis. Deficiencies with these approaches are identified. A new approach is proposed that combines the results of several imperfect reference tests to define a better reference standard. We call this the composite reference standard (CRS). Using the CRS, accuracy can be assessed using multi-stage sampling designs. Maximum likelihood estimates of accuracy and expressions for the variance of sensitivity and specificity are provided. Data from clinical literature on the detection of Chlamydia trachomatis are used to illustrate and compare the different approaches. Advantages of the CRS relative to other approaches include that the CRS is explicitly defined, does not depend on the results of the new test under investigation, and is easy to interpret.

Evaluation of an in-house polymerase chain reaction for detection of Neisseria gonorrhoeae in urogenital samples

AIM

To develop and evaluate a one day in-house polymerase chain reaction (PCR) assay for the detection of Neisseria gonorrhoeae DNA in urogenital samples.

METHODS

429 urogenital specimens were tested for the presence of N gonorrhoeae by in-house PCR and by Gen-Probe. The PCR assay amplifies target sequences within the N gonorrhoeae cppB gene on the 4.2 kb cryptic plasmid, after which amplicons are detected by a streptavidinbiotin based enzyme immunoassay using an internal probe. Discordant specimens were further evaluated by repeating the PCR and the Gen-Probe assay, and by an additional PCR using another set of 16S primers followed by radioactive detection of amplicons on a Southern blot.

RESULTS

Of the 429 samples tested, 15 were found positive by in-house PCR, eight of which were confirmed by Gen-Probe. Of the seven discrepant samples, five were confirmed by 16S PCR and are also considered true positive. The remaining two samples were positive in the in-house PCR only, and are considered false positive. After resolution of discrepant samples, the sensitivities of the N gonorrhoeae assays were 100% and 61.5% for the in-house PCR and Gen-Probe, respectively, while specificities were comparable at 99.5% and 100%.

CONCLUSIONS

The in-house PCR for the detection of N gonorrhoeae DNA is at least comparable to Gen-Probe in performance. An extended evaluation period should elucidate if the additional five GO-PCR positive specimens, confirmed by 16S PCR, are caused by persistence of DNA or whether the method is indeed more sensitive.

Multicenter evaluation of the fully automated COBAS AMPLICOR PCR test for detection of Chlamydia trachomatis in urogenital specimens

The fully automated COBAS AMPLICOR CT/NG test for the detection of Chlamydia trachomatis was evaluated in a multicenter trial. Test performance was evaluated for 2,014 endocervical swab and 1,278 urine specimens obtained from women and for 373 urethral swab and 254 urine specimens obtained from men. Culture served as the reference test. Culture-negative, COBAS AMPLICOR-positive specimens that tested positive in a confirmatory PCR test for an alternative target sequence within the C. trachomatis major outer membrane protein gene were resolved as true positives. The overall prevalence of chlamydia was 4.3% in cervical swabs and 11.0% in urethral swabs from men. When the results for each specimen type were considered separately, the resolved sensitivities were 96.5% (83 of 86) for endocervical swab specimens, 95.1% (39 of 41) for urine specimens from women, 100.0% (41 of 41) for urethral swab specimens from men, and 94.4% (17 of 18) for urine specimens from men; the resolved specificities were 99.4% (1,912 of 1,924) for endocervical swab specimens, 99.8% (1,204 of 1,207) for urine specimens from women, 98. 5% (325 of 330) for urethral swab specimens from men, and 100.0% (236 of 236) for urine specimens from men. For the subset of patients from whom both swab and urine specimens were collected, the combined results for both specimen types were used to identify all infected patients. Using these combined reslts as criteria, the resolved sensitivities for the COBAS AMPLICOR test were 82.6% (38 of 46) for endocervical swab specimens, 84.4% (38 of 45) for urine specimens from women, 84.2% (16 of 19) for urethral swab specimens from men, and 89.5% (17 of 19) for urine specimens from men. In comparison, the sensitivity of culture was only 56.5% (26 of 46) for endocervical specimens and 63.2% (12 of 19) for urethral specimens from men. The internal control provided in the COBAS AMPLICOR test revealed that 2.9% of specimens were inhibitory when they were initially tested. Nevertheless, valid results were obtained for 99. 1% of specimens because 68.7% of the inhibitory specimens were not inhibitory when a second aliquot of the original sample was tested. Two additional COBAS AMPLICOR-positive specimens were detected by retesting inhibitory specimens. The COBAS AMPLICOR CT/NG test for the detection of C. trachomatis exhibited equally high sensitivities and specificities with both urogenital swab and urine specimens and, thus, is well-suited for use in screening.

Evaluation of the abbott LCx assay for detection of Neisseria gonorrhoeae in endocervical swab specimens from females

The Abbott LCx Neisseria gonorrhoeae assay (Abbott Laboratories, Abbott Park, Ill.) uses a ligase chain reaction (LCR) amplification in the LCx probe system for detection of a specific nucleotide sequence in the Opa-encoding gene of N. gonorrhoeae. We evaluated the LCx assay in a comparison with conventional culture employing modified Thayer-Martin media for the detection of N. gonorrhoeae from female endocervical specimens obtained from patients attending a sexually transmitted disease clinic. Discordantly LCR-positive and culture-negative specimens were further evaluated by testing with another LCR assay which used an N. gonorrhoeae-specific pilin probe. Specimens positive by both LCR assays were considered confirmed LCx-positive specimens. A specimen was considered to contain N. gonorrhoeae when it was either culture positive or culture negative and confirmed LCx positive. A total of 403 female endocervical specimens were evaluated. The prevalence of N. gonorrhoeae in this population was 8.7%. The sensitivity and specificity of the LCx assay were 94.3 and 99.4%, and those of culture were 77.1 and 100%, respectively. The Abbott LCx assay is a rapid, sensitive method for detection of N. gonorrhoeae in female endocervical specimens.

Detection of Neisseria gonorrhoeae infection by ligase chain reaction testing of urine among adolescent women with and without Chlamydia trachomatis infection

BACKGROUND AND OBJECTIVES

Culture, the conventional method for detection of Neisseria gonorrhoeae, requires invasive sampling and stringent specimen transport conditions. The recently developed ligase chain reaction test (LCR; Abbott Laboratories; North Chicago, IL) allows noninvasive sampling and stable transport conditions, but has not been evaluated with specimens from adolescent populations.

GOAL OF THIS STUDY

To perform a comparative evaluation of a commercial LCR test and culture for the diagnosis of N. gonorrhoeae in adolescent women.

STUDY DESIGN

Urine and endocervical swab specimens from 330 teenage women seen in two public health adolescent clinics were tested by LCR and culture. For resolution of discordant results, a polymerase chain reaction (PCR) test was developed that directly amplifies N. gonorrhoeae DNA from urine samples processed for LCR.

RESULTS

Thirty-one of 330 (9.4%) cervical specimens were culture-positive for N. gonorrhoeae, and 30 of 330 (9.1%) urine specimens were positive by LCR. After resolution of 13 discordant results, the sensitivity, specificity, and positive and negative predictive values of LCR for urine were 88.2%, 100%, 100%, 98.7%, respectively, and for culture of endocervical specimens were 82.3%, 98.9%, 90.3% and 98%, respectively.

CONCLUSIONS

Although more expensive than culture, LCR offers a sensitive means for the detection of N. gonorrhoeae in urine samples and may be useful for this purpose in settings where pelvic examinations are difficult to perform and simultaneous detection of N. gonorrhoeae and Chlamydia trachomatis is advantageous.

Evaluation of the Abbott LCx ligase chain reaction assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine and genital swab specimens from a sexually transmitted disease clinic population

The Abbott LCx ligase chain reaction (LCR) assay for the simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae was evaluated by using swab and urine specimens from 562 patients. C. trachomatis results by LCR were compared to those by the Gen-Probe PACE 2 assay, whereas N. gonorrhoeae results by LCR were compared to those by culture. The Gen-Probe and LCR assays were performed according to the manufacturers' instructions. Gram-negative diplococci growing on modified Thayer-Martin medium were confirmed as N. gonorrhoeae by the GonoGen II assay. Supplemental data analysis was performed by major outer membrane protein PCR for C. trachomatis and probes for pilin gene detection for N. gonorrhoeae. A true-positive result for each pathogen was defined as a positive result for all three or two of three assays. Overall agreement among the six assays was 94.8%. C. trachomatis prevalence was 16.2%; N. gonorrhoeae prevalence was 5.5%. The overall sensitivity and specificity, respectively, for each test (after supplemental data analysis) were as follows: for C. trachomatis, Gen-Probe, 65.9 and 100%; LCR on urine, 90.1 and 100%; LCR on swab specimens, 96.7 and 100%; and for N. gonorrhoeae, culture, 80.6 and 100%; LCR on urine, 93.5 and 99.8%; and LCR on swab specimens, 96.8 and 100%. For women, the N. gonorrhoeae culture was very insensitive compared to its performance in men (58.3 versus 94.7%, respectively). For C. trachomatis, the Gen-Probe assay's sensitivity was lower for men than for women (62.3 versus 71.1%, respectively). The sensitivity for C. trachomatis detection by LCR on urethral and cervical swab specimens was 96.2 and 97.4% for men and women, respectively. For men, swab results were slightly better than urine results for both pathogens (sensitivity for C. trachomatis in swab and urine specimens, 96.2 and 92.5%, respectively; sensitivity for N. gonorrhoeae in swab and urine specimens, 100 and 94.7%, respectively), while for women, cervical swabs were superior in sensitivity to urine samples for detecting C. trachomatis (swab, 97.4%; urine, 81.6%) and equivalent for N. gonorrhoeae (swab, 92.3%; urine, 91.6%). The LCx LCR appears to be both sensitive and specific for the detection of C. trachomatis and N. gonorrhoeae when performed on urine or genital swab samples. Swab samples had better sensitivity than urine samples for the detection of both pathogens.

Bias in discrepant analysis: when two wrongs don't make a right

Imperfect reference standards (alloyed standards) often hinder evaluation of new diagnostic tests. Discrepant analysis, a two-stage modification of the standard evaluation of diagnostic tests, has been used to circumvent this problem. In discrepant analysis, additional testing is performed to resolve discrepant results of the new diagnostic test and the alloyed standard. This article demonstrates algebraically that sensitivity and specificity will be overestimated by discrepant analysis, even when a perfect gold standard is used to resolve the discrepant results. The magnitude of the bias depends on the true sensitivity and specificity of the new test and initial alloyed standard, the prevalence of disease in the study population, and the proportion of concordant errors between the two tests. The article also demonstrates substantial bias associated with the use of alloyed standard tests in both stages of discrepant analysis. This procedure should not be used routinely for evaluation of diagnostic tests.

Comparison of Roche Cobas Amplicor and Abbott LCx for the rapid detection of Chlamydia trachomatis in specimens from high-risk patients

OBJECTIVE

To evaluate two automated amplification systems for the detection of Chlamydia trachomatis in urogenital specimens, the Cobas Amplicor (Roche Diagnostic Systems, Branchburg, NJ) and the LCx (Abbott Laboratories, Abbott Park, IL).

STUDY DESIGN

The two systems were compared testing specimens from 302 high-risk patients, including 98 female cervical swab specimens and 204 male urine specimens. The patients attended the state STD clinic in Reykjavik, Iceland, either because of symptoms or as a result of contract tracing.

RESULTS

The prevalence of C. trachomatis infection was 15.3% in women and 13.2% in men. For the male urine specimens, the sensitivity and specificity were 100% and 99.4% for the Cobas Amplicor and 74.1% and 100% for the LCx. In the cervical swabs, both systems detected all 15 true-positive specimens. The internal control used with the Cobas Amplicor detected inhibition in 2% of the male urine and 20% female cervical swabs, respectively.

CONCLUSION

The Cobas Amplicor demonstrated slightly better sensitivity than LCx in male urine specimens. Both systems offer the benefits of automation for routine diagnostic testing.

An internal control for routine diagnostic PCR: design, properties, and effect on clinical performance

We constructed internal controls (ICs) to provide assurance that clinical specimens are successfully amplified and detected. The IC nucleic acids contain primer binding regions identical to those of the target sequence and contain a unique probe binding region that differentiates the IC from amplified target nucleic acid. Because only 20 copies of the IC are introduced into each test sample, a positive IC signal indicates that amplification was sufficient to generate a positive signal from targets present at the limit of test sensitivity. The COBAS AMPLICOR Chlamydia trachomatis, Neisseria gonorrhoeae, Mycobacterium tuberculosis, and human hepatitis C virus tests exhibited inhibition rates ranging from 5 to 9%. Approximately 64% of these inhibitory specimens were not inhibitory when a second aliquot was tested. Because repeatedly inhibitory specimens were not reported as false negative and because additional infected specimens were detected during retesting, test sensitivities were 1 to 6% greater than they would have been if the IC had not been used.

Randomised trials of STD treatment for HIV prevention: report of an international workshop. HIV/STD Trials Workshop Group

Three community trials of the impact of STD treatment interventions on HIV incidence in rural populations have been completed or are in progress in Uganda and Tanzania. Investigators from these trials met for a joint technical workshop in Baltimore in May 1996. This report summarises the consensus of the workshop, with the aim of providing useful input to research on HIV intervention strategies. Issues discussed include: (i) the role of community randomised trials; (ii) strategies for STD management; (iii) epidemiological and statistical issues in the design and analysis of community randomised trials; (iv) diagnostic methods for STDs in population surveys; (v) treatment regimens for STDs in rural Africa; and (vi) ethical issues in community trials.

Diagnosis of Neisseria gonorrhoeae infections in women by using the ligase chain reaction on patient-obtained vaginal swabs

The increased sensitivities of nucleic acid amplification tests such as ligase chain reaction (LCR) have the potential to simplify specimen collection for gonorrhea diagnosis. In this study patients took their own vaginal swab specimens for gonorrhea culture and LCR testing. Immediately following specimen collection by patients, a trained clinician obtained endocervical swab specimens for the same tests. By using LCR to diagnose gonorrhea, 54 (17.5%) of 309 patients had positive tests. Forty-five patients with positive cervical LCR tests also had positive vaginal LCR tests; for one patient, only a cervical LCR specimen was positive, and for eight patients, only vaginal specimens were positive. For specimens from patients whose gonorrhea cultures were positive, all vaginal swab specimens were positive by LCR and 42 (91%) of 46 cervical swab specimens were positive by LCR. LCR-positive specimens from eight patients with negative cultures (four with positive vaginal specimens only, one with a positive cervical specimen only, and three with positive vaginal and cervical specimens) were further evaluated with unrelated probe sets for gonococcal pilin B. Following resolution of the discrepancies between culture-negative and LCR-positive specimens, a diagnosis of gonorrhea could be confirmed for 52 of 54 patients with positive LCR tests. LCR testing with vaginal swabs was 100% sensitive and 99.6% specific and had a positive predictive value of 98.1% and a negative predictive value of 100%. In this study LCR testing of vaginal swab specimens obtained by patients themselves was significantly more sensitive for gonorrhea diagnosis of women than cervical LCR or culture (100% versus 84.6% for cervical LCR or culture; Mantel-Haenszel chi-square test result, 8.58; P = 0.003).

Detection of Neisseria gonorrhoeae and Chlamydia trachomatis in genitourinary specimens from men and women by a coamplification PCR assay

A coamplification PCR test for the direct detection of Neisseria gonorrhoeae and Chlamydia trachomatis in urethral and endocervical swabs and urine samples from men and women was compared to standard culture techniques. Processed specimens were amplified in single reaction tubes containing primers for both organisms, and PCR products were detected by a colorimetric microwell plate hybridization assay specific for each pathogen. Of 344 specimens from men, 45 (13.1%) urine specimens were PCR positive for C. trachomatis, 51 (14.8%) urethral swab specimens were PCR positive, and 29 urethral swab specimens (8.4%) were culture positive. After analysis of discrepancies, the resolved sensitivity and specificity of PCR for C. trachomatis were 96.2 and 99.3%, respectively, in urethral swab specimens, compared to 88.2 and 98.6% for urine specimens. Of the 192 specimens from women, 28 (14.6%) urine specimens were PCR positive for C. trachomatis, 32 (16.7%) endocervical specimens were PCR positive, and 19 (9.9%) endocervical specimens were culture positive. After analysis of discrepancies, the resolved sensitivity and specificity of PCR for C. trachomatis for endocervical specimens were both 100% compared to 100 and 99.4%, respectively, for urine specimens from women. In men, 68 (19.8%) urine specimens were PCR positive for N. gonorrhoeae, 73 (21.2%) urethral swabs were PCR positive, and 59 (17.2%) urethral swabs were culture positive. After analysis of discrepancies, the resolved sensitivity and specificity of PCR for N. gonorrhoeae were 97.3 and 97.0%, respectively, for urethral specimens compared to 94.4 and 98.5% for urine specimens. In women, 18 (9.4%) urine specimens were PCR positive for N. gonorrhoeae, 23 (12.0%) were endocervical swab PCR positive, and 15 (7.8%) endocervical specimens were culture positive. After analysis of discrepancies, the resolved sensitivity and specificity of PCR for N. gonorrhoeae were 100 and 99.4%, respectively, for endocervical specimens compared to 90.0 and 95.9% for female urine specimens. These results indicate that a multiplex PCR is highly sensitive for detecting both C. trachomatis and N. gonorrhoeae from a single urine or genital swab, providing a more cost-effective way of screening multiple pathogens.

Comparison of ligase chain reaction and culture for detection of Neisseria gonorrhoeae in genital and extragenital specimens

In addition to the urogenital tract, Neisseria gonorrhoeae infects extragenital sites such as the pharynx and anorectal canal. Culture and a ligase chain reaction (LCR)-based assay were compared for their performance for the diagnosis of N. gonorrhoeae infection with specimens from various urogenital and extragenital sites of 200 men and 125 women. The sensitivity and specificity of the LCR assay with male urethral swabs were both 100%, compared to values of 95.9 and 100%, respectively, for culture of urethral swabs or 98.0 and 100%, respectively, for LCR with first-void urine (FVU). For women, LCR with FVU showed the highest sensitivity (94.7%), and culture of urethral samples showed the lowest sensitivity (63.2%) (P < 0.05). In a selected subgroup of 47 men and 22 women at increased risk, the rates of pharyngeal infection were 15 and 18%, respectively, and those of anorectal infection were 13 and 45%, respectively. The sensitivity of LCR was greater than that of culture for both pharyngeal and anorectal specimens. Thus, the overall performance of LCR testing with swabs or FVU was better than that of culture for the diagnosis of genital or extragenital gonorrhea.

Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by ligase chain reaction-based assays with clinical specimens from various sites: implications for diagnostic testing and screening

Ligase chain reaction (LCR)-based tests for the diagnosis of Chlamydia trachomatis and Neisseria gonorrhoeae infections in men and women attending a sexually transmitted disease clinic were evaluated. LCR testing of urethral swab and urine specimens from men and cervical swab and urine specimens from women was compared with culture of male urethral swabs and female cervical and urethral swabs, respectively. An expanded "gold standard" was defined as a positive culture or at least one specimen confirmed to be positive by LCR testing. The prevalence of C. trachomatis infection as detected by cell culture was 7.0% among 614 men and 5.0% among 602 women. By LCR, these values increased to 11.4 and 9.9% with urethral swabs and urine, respectively, for men and 9.6 and 9.1% with cervical swabs and urine, respectively, for women. Relative to the expanded gold standard, the sensitivity of cell culture with male urethral swabs or female cervical swabs was 57.3 and 45.5%, respectively, compared with corresponding values of 93.3 and 87.9% for LCR. The sensitivity of LCR with urine specimens was 77.3 and 78.8% for men and women, respectively. The prevalence of N. gonorrhoeae infection as detected by culture was 5.9% among 220 men and 2.9% among 383 women. The corresponding values were 8.2 and 5.5%, respectively, by LCR testing of swabs. Prevalence values by LCR testing of urine were 7.3% for men and 2.9% for women. The sensitivity of culture was 72.2% for men and 50.0% for women. The sensitivities of LCR were 100% with male urethral swabs, 95.4% with female cervical swabs, 88.9% with male urine, and 50.0% with female urine. These results indicate that the LCR-based assays represent a major improvement in C. trachomatis and N. gonorrhoeae diagnostics. The sensitivity of testing of urethral or cervical swabs by LCR was markedly greater than that by culture. The sensitivity of testing female or male urine specimens was equal to or greater than that of culturing cervical or urethral specimens. LCR testing of urine specimens may prove useful for screening for C. trachomatis.