Nucleic acid amplification testing for Neisseria gonorrhoeae: an ongoing challenge

Time from first intercourse to first sexually transmitted infection diagnosis among adolescent women

OBJECTIVE

To determine the time between first intercourse and first sexually transmitted infection (STI) with Chlamydia trachomatis, Neisseria gonorrhoeae, or Trichomonas vaginalis and time between repeated infections.

DESIGN

Observational study.

SETTING

Three adolescent medicine clinics.

PARTICIPANTS

A cohort of 386 urban young women aged 14 to 17 years at enrollment.

MAIN OUTCOME MEASURES

Age at first intercourse; organism-specific interval between first intercourse and first STI diagnosis; interval between repeated infections; and age at first STI test prior to study participation.

RESULTS

Participants had first intercourse at a young age (first, second, and third quartiles were 13, 14, and 15 years of age, respectively). By age 15 years, 25% of the women acquired their first STI, most often C trachomatis. Median interval between first intercourse and first STI diagnosis was 2 years. Within 1 year of first intercourse, 25% had their first C trachomatis infection. Repeated infections were common; within 3.6, 6, and 4.8 months, 25% of the women with prior C trachomatis, N gonorrhoeae, and T vaginalis infection were reinfected with the respective organisms. Considerable delay in STI testing was found for those who began sex at a younger age. The median interval between first sex and first test were 4.9, 3.5, 2.1, 1.8, and 1.2 years for those who had first sex at ages 10, 11, 12, 13, and 14 years, respectively.

CONCLUSIONS

Timely screening and treatment are important for prevention of STI sequelae. For urban adolescent women, STI screening (especially for C trachomatis) should begin within a year after first intercourse and infected individuals should be retested every 3 to 4 months.

Repeated Chlamydia trachomatis genital infections in adolescent women

BACKGROUND

Repeated Chlamydia trachomatis infections are common among young sexually active women. The relative frequency of reinfection and antibiotic treatment failure is undefined.

METHODS

Adolescent women enrolled in a longitudinal cohort had behavioral and sexually transmitted infection assessments performed every 3 months, including amplification tests for C. trachomatis, ompA genotyping, and interviews and diary entries to document sex partner-specific coitus and event-specific condom use. Repeated infections were classified as reinfection or treatment failure by use of an algorithm. All infections for which treatment outcomes were known were used to estimate the effectiveness of antibiotic use.

RESULTS

We observed 478 episodes of infection among 210 study participants; 176 women remained uninfected. The incidence rate was 34 episodes/100 woman-years. Of the women who were infected, 121 experienced 1 repeated infections, forming 268 episode pairs; 183 pairs had complete data available and were classified using the algorithm. Of the repeated infections, 84.2% were definite, probable, or possible reinfections; 13.7% were probable or possible treatment failures; and 2.2% persisted without documented treatment. For 318 evaluable infections, we estimated 92.2% effectiveness of antibiotic use.

CONCLUSIONS

Most repeated chlamydial infections in this high-incidence cohort were reinfections, but repeated infections resulting from treatment failures occurred as well. Our results have implications for male screening and partner notification programs and suggest the need for improved antibiotic therapies.

Detecting and treating common sexually transmitted diseases

In the UK, many sexually transmitted infections (STIs) are best managed in conjunction with an appropriate specialist, for example, a genitourinary medicine practitioner or a Microbiologist. In most of the world, however, gynaecologists routinely manage STIs in women. This article focuses on the most important infections in women, and those in which management is changing. It also addresses the current status, and new developments around the syndrome of pelvic inflammatory disease (PID), which essentially is an STI.

Diagnosis, management and prevalence estimation of gonorrhoea: influences of Aptima Combo 2 assay with alternative target confirmation

Case-notes and laboratory data were retrospectively reviewed for influences of dual testing by Aptima Combo 2 (AC2) for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) on the diagnosis, management and prevalence estimation of gonorrhoea in the genitourinary (GU) medicine clinic and community. NG positives by AC2 were confirmed by Aptima Gonococcus assay. Unconfirmed positives were rare. Our study showed that in the GU medicine clinic, AC2 detected about 20% extra cases of NG beyond culture. For best standard of care, NG culture and microscopy are still required in some patients to ensure that treatment is rapid and appropriate. Compared to self-referral at the GU medicine clinic, community tests made a substantial contribution to the overall number of NG cases found (40 community versus 35 Macclesfield GU medicine clinic). The ratio of female to male NG cases found was significantly higher (P = 0.002) in the community (13 M, 27 F) than at the GU medicine clinic (25 M, 10 F). In the community, over 60% of NG infections occurred in chlamydia-negative patients. The overall prevalence of NG in the GU medicine clinic was 1.3%, the true prevalence being much lower at 0.9% on primary test. Prevalence in the community was 0.4%. Data from dual testing in the community can clarify NG prevalence beyond the existing KC60 (sexually transmitted infections) reports.

Epidemiology of sexually transmitted infections in suspected child victims of sexual assault

OBJECTIVE

The objective of this study was to describe the epidemiology of Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis, Treponema pallidum, HIV, and herpes simplex virus type 2 (HSV-2) infection diagnosed by culture or by serologic or microscopic tests and by nucleic acid amplification tests in children who are evaluated for sexual victimization.

METHODS

Children aged 0 to 13 years, evaluated for sexual victimization, who required sexually transmissible infection (STI) testing were enrolled at 4 US tertiary referral centers. Specimens for N gonorrhoeae and C trachomatis cultures, wet mounts for detection of T vaginalis, and serologic tests for syphilis and HIV were collected and processed according to study sites' protocols. Nucleic acid amplification tests for C trachomatis and N gonorrhoeae and serologic tests for HSV-2 were performed blinded to other data.

RESULTS

Of 536 children enrolled, 485 were female. C trachomatis was detected in 15 (3.1%) and N gonorrhoeae in 16 (3.3%) girls. T vaginalis was identified in 5 (5.9%) of 85 girls by wet mount, 1 (0.3%) of 384 children had a positive serologic screen for syphilis, and 0 of 384 had serologic evidence of HIV infection. Of 12 girls who had a specimen for HSV-2 culture, 5 (41.7%) had a positive result; 7 (2.5%) of 283 had antibody evidence of HSV-2 infection. Overall, 40 (8.2%) of 485 girls and 0 of 51 boys (P = .02) had >or=1 STI. Girls with vaginal discharge were more likely to test positive for an STI (13 [24.5%] of 53) than other girls (27 [6.3%] of 432; prevalence ratio = 3.9; P < .001), although 10 girls with STIs had normal physical examinations. Most girls (27 [67.5%]) with a confirmed STI had normal or nonspecific findings on anogenital examination.

CONCLUSIONS

The prevalence of each STI among sexually victimized children is <10%, even when highly sensitive detection methods are used. Most children with STIs have normal or nonspecific findings on physical examination.

Simple, rapid, and inexpensive detection of Neisseria gonorrhoeae resistance mechanisms using heat-denatured isolates and SYBR green-based real-time PCR

Neisseria gonorrhoeae has developed resistance to multiple classes of antimicrobials. There is now growing concern that without the availability of appropriate public health strategies to combat this problem, gonorrhea could become untreatable. For this reason, surveillance for gonococcal antimicrobial resistance must be optimal both in terms of obtaining a representative sample of gonococcal isolates and in terms of having the appropriate tools to identify resistance. To aid with this surveillance, molecular tools are increasingly being used. In the present study, we investigated the use of a simple heat denaturation protocol for isolate DNA preparation combined with SYBR green-based real-time PCR for the identification of mutations associated with N. gonorrhoeae antimicrobial resistance. A total of 109 clinical gonococcal isolates were tested by high-resolution melting (HRM) curve analysis for chromosomal mutations associated with gonococcal resistance to beta-lactam antibiotics: a penA 345A insertion, ponA L421P, mtrR G45D, substitutions at positions 120 and 121 in porB1b, and an adenine deletion in the mtrR promoter. An allele-specific PCR assay was also investigated for its ability to detect the adenine deletion in the mtrR promoter. The results were compared to those obtained by DNA sequencing. Our HRM assays provided the accurate discrimination of heat-treated isolates in which the sequence types differed in GC content, including isolates with the penA 345A insertion and the ponA L421P and mtrR G45D mutations. The allele-specific PCR assay accurately identified isolates with the adenine deletion in the mtrR promoter. Heat-denatured DNA combined with SYBR green-based real-time PCR offers a simple, rapid, and inexpensive means of detecting gonococcal resistance mechanisms. These methods may have broader application in the detection of polymorphisms associated with phenotypes of interest.

Molecular tests for human papillomavirus (HPV), Chlamydia trachomatis and Neisseria gonorrhoeae in liquid-based cytology specimen

BACKGROUND

Laboratory detection of Human papillomavirus (HPV), Chlamydia trachomatis and Neisseria gonorrhoeae in liquid-based cervicovaginal cytology specimens is now based on identification of the DNA sequences unique to these infectious agents. However, current commercial test kits rely on nucleotide probe hybridization to determine DNA sequences, which may lead to diagnostic errors due to cross-reactivity. The aim of this study was to find a practical approach to perform automated Sanger DNA sequencing in clinical laboratories for validation of the DNA tests for these three infectious agents.

METHODS

A crude proteinase K digest of 5% of the cells collected in a liquid-based cervicovaginal cytology specimen was used for the detection of DNA molecules specific for HPV, C trachomatis and N gonorrhoeae, and for preparation of materials suitable for direct automated DNA sequencing. Several sets of commercially available polymerase chain reaction (PCR) primers were used to prepare nested PCR amplicons for direct DNA sequencing.

RESULTS

Some variants of HPV-16 and HPV-31 were found to share an at least 34-base long sequence homology downstream of the GP5+ binding site, and all HPV-6 and HPV-11 variants shared an upstream 34-base sequence including part of the GP5+ primer. Accurate HPV genotyping frequently required more than 34-bases for sequence alignments to distinguish some of the HPV genotype variants with closely related sequences in this L1 gene hypervariable region. Using the automated Sanger DNA sequencing method for parallel comparative studies on split samples and to retest the residues of samples previously tested positive for C trachomatis and/or for N gonorrhoeae, we also found false-negative and false-positive results as reported by two commercial nucleic acid test kits.

CONCLUSION

Identification of a signature DNA sequence by the automated Sanger method is useful for validation of HPV genotyping and for molecular testing of C trachomatis and N gonorrhoeae in liquid-based cervicovaginal Papanicolaou (Pap) cytology specimens for clinical laboratories with experience in molecular biology to increase the specificity of these DNA-based tests. However, even a highly specific test for high-risk HPV genotyping may have unacceptably low positive predictive values for precancer lesion in populations with a low cervical cancer prevalence rate.

Neisseria gonorrhoeae infection in urban Sydney women: prevalence and predictors

Background: The notification rate of female gonorrhoea in urban Sydney is very low. With the increasing use of nucleic acid amplification tests (NAAT), demonstrating a low prevalence of gonorrhoea in women would have important implications for the reliability of positive results. We determined the prevalence of female cervical gonorrhoea in our urban sexual health clinic and identified associated clinical, behavioural and demographic variables that may allow more targeted screening practices. Methods: The Sydney Sexual Health Centre database was used to identify women tested for cervical gonorrhoea between 1997 and 2007. Diagnostic, demographic and behavioural information were extracted to ascertain the prevalence of gonorrhoea and describe variables associated with infection. Additionally, a case control study was conducted of cervical gonorrhoea cases from January 2000 to December 2005, with two gonorrhoea negative women selected for each case as controls. A blinded researcher examined each medical record to determine genital symptoms, being a contact of gonorrhoea, sex work, sex outside of Australia, injecting drug use. Results: Between 1997 and 2007, 77 women were diagnosed with cervical gonorrhoea, a prevalence of 0.37%. Results of the case control study reveal that women with gonorrhoea were more likely to be symptomatic [odds ratio (OR) 3.7, 95% confidence interval (CI) 1.7–8.4], be a known contact of gonorrhoea (OR 264, 95% CI 149–470), or have had recent sex overseas, or with a partner from overseas (OR 1.75, 95% CI 1.11–2.75). Conclusion: Cervical gonorrhoea infection is rare in our urban sexual health clinic, and even more unlikely in asymptomatic women without risk factors. This low prevalence of gonorrhoea, particularly in asymptomatic women, decreases the reliability of positive NAAT test results. This has important implications for the screening of asymptomatic women presenting to urban sexual health clinics in Australia.

Evaluation of self-collected vaginal swab, first void urine, and endocervical swab specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in adolescent females

OBJECTIVE

To assess the concordance of self-obtained vaginal swabs (SVS), first void urine samples (FVU) and provider-collected endocervical swabs (PES) for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhea (NG) in adolescents.

METHODS

A total of 342 adolescent women and 1080 baseline and semi-annual visits were analyzed. FVU, SVS and PES were collected at each biannual visit. All specimens were tested by BDProbeTec ET(trade mark) Amplified DNA Assay. Sensitivity, specificity, positive predictive value (PPV) negative predictive value (NPV) and kappa coefficient were calculated to evaluate the ability to identify possible infected cases using samples from three anatomic sites and the test agreement between any two of these three specimen types. Positive results from at least two of the three specimens collected from same subject at the same study visit was considered true positive.

RESULTS

The positivity rates for CT and NG were 26.6 and 11.7 per 100 women respectively. The sensitivities of SVS, FVU and PES for detecting CT were 97.3%, 89.2% and 90.1% respectively. For the detection of NG, the sensitivities of the three sampling methods were 100%, 88.6% and 95.5% respectively. The specificities were between 94.7% and 99.7% for both CT and NG. Kappa coefficients of CT test results were 0.89, 0.88 and 0.83 for specimen pairs SVSvsPES, SVSvsFVU and PESvsFVU respectively. For the detection of NG, kappa coefficients were 0.91, 0.87 and 0.91 for these three pairs (all P<0.0001). Kappa>0.75 is considered excellent agreement between specimens.

CONCLUSION

There were strong agreements among SVS, PES and FVU specimens on the detection of CT and NG infections in adolescent females using nucleic acid amplification test. SVS represented as high as or more sensitive an approach for detecting both CT and NG compared to PES. Although FVU was the least sensitive sampling method, it is also the least invasive method. Thus SVS and FVU may provide a reliable alternative to endocervical specimens for CT and NG screening.

Application of atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry for rapid identification of Neisseria species

Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI MS) was applied to develop a proteomics-based method to detect and identify Neisseria species. Heat-inactivated clinical isolate cell suspensions of Neisseria gonorrhoeae and strains belonging to five serogroups (A, B, C, W135, and Y) of Neisseria meningitidis were subjected to on-probe protein/peptide extraction and tryptic digestion followed by AP-MALDI tandem MS (MS/MS)-based proteomic analysis. Amino acid sequences derived from three protonated peptides with m/z values of 1743.8, 1894.8, and 1946.8 were identified by AP-MALDI MS/MS and MASCOT proteome database search analysis as belonging to neisserial acyl carrier protein, neisserial-conserved hypothetical protein, and neisserial putative DNA binding protein, respectively. These three peptide masses can thus be potential biomarkers for neisserial species identification by AP-MALDI MS.

Comparison of microscopy, culture and in-house PCR and NASBA assays for diagnosis of Neisseria gonorrhoeae in Russia

This study aimed to assess the laboratory diagnosis of Neisseria gonorrhoeae in St. Petersburg, Russia. In total, 334 consecutive symptomatic patients were enrolled. Cervical and urethral specimens from women (n=286) and urethral specimens from men (n=48) were analyzed by microscopy, culture and two in-house NAATs, i.e. polymerase chain reaction (PCR) and nucleic acid sequence-based amplification (NASBA), developed in Russia. All N. gonorrhoeae-positive samples were confirmed using porA pseudogene and 16S rRNA gene sequencing. All methods displayed 100% specificity, i.e. positive predictive values of 100%. Compared to the PCR (most sensitive method in the present study), in women the sensitivity of both microscopy and culture was 31.8%, and that of NASBA was 90.9%. In men, microscopy, culture and NASBA displayed a sensitivity of 75%, 50% and 100%, respectively. The negative predictive values of microscopy, culture, and NASBA were 97.3%, 97.3%, and 99.6% in women, and 97.8%, 95.7%, and 100% in men, respectively. According to the PCR, the prevalences of N. gonorrhoeae were 4.5% (women) and 8.3% (men). In conclusion, both the investigated Russian NAATs displayed a high sensitivity and specificity. However, in general the diagnosis of gonorrhoea in Russia is suboptimal and crucially requires validation, improvements and quality assurance.

Exploring 'best practice' for nucleic acid detection of Neisseria gonorrhoeae

Nucleic acid detection tests (NADT) have considerable benefits for the detection of Neisseria gonorrhoeae (GC), including high sensitivity across a range of specimen types and use under widely differing settings and conditions. However, sexual health practitioners and others who use data generated by NADT for GC should be aware of some important limitations of these tests. False-positive results caused by cross reaction with commensal Neisseria species have been observed in many assays, and have lead to unacceptably low positive-predictive values in some patient populations. Further, false-negative results can be caused by GC sequence variation, with some gonococci lacking certain NADT target sequences. This review examines the issues associated with gonococcal NADT and considers best practice for use of these assays based on current knowledge. We emphasise the need for supplementary testing and extensive assay validation, and suggest appropriate strategies for these requirements irrespective of the setting in which they are used. Further, we highlight the need to maintain culture-based testing for certain specimen sites as well as for antimicrobial resistance surveillance.

A duplex Neisseria gonorrhoeae real-time polymerase chain reaction assay targeting the gonococcal porA pseudogene and multicopy opa genes

Cross-reactions of gonococcal nucleic acid amplification tests (NAATs) with commensal Neisseria strains are well documented. Recent data now indicate that sequence-related false-negative results can occur in gonococcal NAATs, whereby target sequences either are absent or contain several mutations. In this study, a duplex Neisseria gonorrhoeae real-time polymerase chain reaction (PCR) (NGduplex) assay targeting the gonococcal porA pseudogene and multicopy opa genes was developed. The NGduplex was evaluated by testing 596 clinical specimens, including 292 urogenital specimens and 304 throat swab specimens. The results were compared with those obtained using a consensus reference standard comprising 3 monoplex real-time PCR assays. The results show that the NGduplex assay is highly suitable for routine screening for gonorrhea, providing an overall clinical sensitivity and specificity of 100% and 99.3%, respectively, for both urogenital and throat swab specimens. In addition, the 2-target system of the NGduplex assay decreases the potential for sequence-related false-negative results and can provide simultaneous confirmation of positive results.

Applications of molecular testing in clinical laboratories for the diagnosis and control of gonorrhea

The potential for enhanced diagnosis and control of gonococcal infection through the application of advances in molecular medicine is now being realized. However, the introduction of diagnostic nucleic acid amplification assays (NAATs) revealed some significant limitations of these applications. Resolution of some, but not all, of these problems has led to recommendations for refined testing algorithms and a better recognition and acceptance of the limitations of NAATs. Resource restriction has limited the use of diagnostic NAATs, especially in less-developed countries where disease rates are highest. However, NAATs have also proved useful in public health approaches to gonorrhea control in all settings. Additional applications including molecular typing of gonococci to identify and interrupt gonococcal transmission chains and definition of antimicrobial resistance patterns in the gonococcus have been proposed. These approaches, especially those for antimicrobial resistance determination, have been less successful for a number of reasons, including their cost and other unresolved issues.

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

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

Non-cultural detection and molecular genotyping of Neisseria gonorrhoeae from a piece of clothing

Isolation of Neisseria gonorrhoeae is currently the gold standard for the definitive diagnosis of gonorrhoea and for use in medico-legal cases in the UK. Molecular detection methods are used increasingly but are untested as evidence of infection in a court of law. An isolate of N. gonorrhoeae was obtained from a child and an article of clothing from an adult male who was suspected of sexual abuse of the child. Biochemical and immunological tests were used to confirm the isolate as N. gonorrhoeae. Amplification by PCR using two targets, cppB and ompIII, was used both as further confirmation of the isolate and to detect the presence of gonococcal-specific DNA from the clothing. The relationship of the gonococcal DNA from the child and the adult was investigated using genotyping (N. gonorrhoeae multi-antigen sequence typing; NG-MAST), including a nested PCR for the por gene. Both samples were indistinguishable by NG-MAST and shared the same sequence type, 403. This is the first report of molecular detection and genotyping of N. gonorrhoeae on an article of clothing, which resulted in conviction of the man for sexual assault.

Evidence that the gonococcal porA pseudogene is present in a broad range of Neisseria gonorrhoeae strains; suitability as a diagnostic target

AIMS

The primary aim of the study was to determine if the gonococcal porA pseudogene is a stable sequence target for the detection of Neisseria gonorrhoeae by PCR.

METHODS

A total of 240 gonococcal strains from various geographic locations were tested by porA pseudogene PCR. In addition, porA pseudogene PCR positivity rates were compared with established gonococcal assays in three Australian states.

RESULTS

All N. gonorrhoeae isolates provided positive results in the porA pseudogene PCR. Positivity rates compared favourably with established gonococcal assays, with increased N. gonorrhoeae detection in the Northern Territory and Western Australia.

CONCLUSIONS

The results of this multicentre study provide further evidence that the porA pseudogene is highly conserved across a diverse range N. gonorrhoeae strains and is a suitable PCR target for routine detection of N. gonorrhoeae.