Detection of Neisseria gonorrhoeae and Chlamydia trachomatis from pooled rectal, pharyngeal and urine specimens in men who have sex with men

Pooled Pharyngeal, Rectal, and Urine Specimens for the Point-of-Care Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Lay Providers in Key Population-Led Health Services in Thailand

Routine testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) in people with heightened risk is lacking in Thailand. This study aimed to assess the performance of the Cepheid Xpert CT/NG assay, conducted by key population (KP) lay providers, for CT and NG detection on single-site and pooled specimens from the pharynx, rectum, and urine. Between August and October 2019, 188 men who have sex with men and 11 transgender women were enrolled. Participants collected urine specimens while trained KP lay providers obtained pharyngeal and rectal swabs. Compared to single-site testing with the Abbott RealTime CT/NG assay by medical technologists, the Xpert assay missed one pharyngeal NG infection out of 199 single-site specimens, giving a 93.3% sensitivity for pharyngeal NG and one missed pharyngeal NG infection out of fifty pooled specimens, giving an 88.9% sensitivity for pharyngeal NG. There was no discrepancy between the two assays for CT detection. The Cohen's Kappa coefficient of pooled specimen testing by the Xpert was 0.93 for NG and 1 for CT when compared to single-site testing by Abbott. Implementing pooled specimen testing by KP lay providers can be a cost-saving strategy to enhance the uptake of CT/NG services for populations facing increased risk.

Using pooled urogenital, anorectal and oropharyngeal specimens to detect Chlamydia trachomatis and Neisseria gonorrhoeae among men who have sex with men in China: a multisite diagnostic accuracy study

OBJECTIVES

Screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) at both urogenital and extragenital sites has been recommended in many countries. Testing of the infections using pooled specimens from urogenital and extragenital sites offer the opportunity to shorten the testing time and reduce the testing cost. Ex-ante pooling is placing the original single-site specimens in a tube with transport media, while ex-post pooling is making a pool of the transport media from both anorectal and oropharyngeal specimens and the urine. This study aimed to conduct a multisite performance evaluation of two pool-specimen approaches (ex-ante and ex-post) in detection of CT and NG using the Cobas 4800 platform among men who have sex with men (MSM) in China.

DESIGN

Diagnostic accuracy study.

SETTING, PARTICIPANTS AND OUTCOME MEASURES

Participants were recruited from MSM communities at six cities in China. Two oropharyngeal and anorectal swabs collected by clinical staff and 20 mL first-void urine collected by the participant himself were used for evaluating sensitivity and specificity.

RESULTS

A total of 1311 specimens were collected from 437 participants in six cities. The sensitivities of ex-ante pooling approach as compared with single-specimen approach (reference standard) were 98.7% (95% CI, 92.7% to 100.0%) for detection of CT and 89.7% (95% CI, 75.8% to 97.1%) for NG, and the specificities were 99.5% (95% CI, 98.0% to 99.9%) and 98.7% (95% CI, 97.1% to 99.6%), respectively. The sensitivities of ex-post pooling approach were 98.7% (95% CI, 92.7% to 100.0%) for CT and 100.0% (95% CI, 91.0% to 100.0%) for NG, and the specificities were 100.0% (95% CI, 99.0% to 100.0%) and 100.0% (95% CI, 99.1% to 100.0%), respectively.

CONCLUSIONS

The ex-ante and ex-post pooling approaches show good sensitivity and specificity in detecting urogenital and extragenital CT and/or NG, indicating that these approaches can be used in epidemiological surveillance and clinical management of CT and NG infections, particularly among MSM population.

Pooling Rectal, Pharyngeal, and Urine Samples to Detect Neisseria gonorrhoeae, Chlamydia trachomatis, and Mycoplasma genitalium Using Multiplex Polymerase Chain Reaction Is as Effective as Single-Site Testing for Men Who Have Sex With Men

Background

Screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) at pharyngeal, urogenital, and anorectal sites is recommended for men who have sex with men (MSM). Pooling samples is a promising technique, but no data are available when pooled screening also includes Mycoplasma genitalium (MG). The main objective of this study was to examine the sensitivity of pooled samples for detecting CT, NG, and MG in MSM using nucleic acid amplification versus single-site testing.

Methods

In this multicenter study, MSM with a positive result for CT, NG, or MG were recalled to the clinic for treatment and were asked to participate in this study. Separate samples were sent to a central virological department that proceeded to form the pooled samples. Testing was performed using the multiplex real-time polymerase chain reaction Allplex STI Essential Assay (Seegene, Seoul, Korea), which can simultaneously detect 7 pathogens.

Results

A total of 130 MSM with at least 1 positive test for CT, NG, or MG were included. A total of 25.4% had a coinfection. The sensitivities of pooled-sample testing were 94.8% for CT, 97.0% for NG, and 92.3% for MG. Pooling failed to detect 8 infections, but pooled-sample analysis missed detecting only samples with a low bacterial load (cycle threshold >35).

Conclusions

Pooling samples from MSM to detect CT, NG, and MG is as sensitive as individual-site testing for these 3 pathogens using the Allplex assay. Missed infections with a very low bacterial load could have a low impact on further transmission.

Clinical Trials Registration. NCT03568695.

Evaluating specimen pooling for Neisseria gonorrhoeae, Chlamydia trachomatis, and Mycoplasma genitalium screening in asymptomatic men who have sex with men

BACKGROUND

Screening for Neisseria gonorrhoeae and Chlamydia trachomatis is recommended for individuals at high-risk for sexually transmitted infections (STIs), while the role of Mycoplasma genitalium screening is still unclear. We evaluated whether specimen pooling is an effective alternative for sexually transmitted infection testing during resource shortages.

METHODS

This 2-year prospective study enrolled 135 asymptomatic patients from a community outreach site who identified as men who have sex with men. Oropharyngeal, urine, and/or rectal swab specimens were pooled and tested using the Aptima Combo 2 assay for Neisseria gonorrhoeae and Chlamydia trachomatis. The Aptima Mycoplasma genitalium assay was performed on 34 patients whose specimens had sufficient sample volume for additional testing. Results from pooled specimens were compared to results obtained by individual-site testing.

RESULTS

The positive percent agreement (PPA) between pooled testing and individual-site testing was 93.8% and negative percent agreement (NPA) was 100% for Neisseria gonorrhoeae. For Chlamydia trachomatis, the PPA was 85.7% and NPA was 99.2%. A PPA of 72.7% and NPA of 95.7% were observed for Mycoplasma genitalium. Discrepancy analysis revealed the majority of false-negative pools were from failure to detect positive rectal samples.

CONCLUSIONS

Specimen pooling reduces sensitivity of the Aptima assays for Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium and thus should be used with caution.

Clinical Performance of the Xpert® CT/NG Test for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae: A Multicenter Evaluation in Chinese Urban Hospitals

Background

We aimed to evaluate the clinical performance of the GeneXpert^® (Xpert) CT/NG assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using urine and cervical swabs collected from patients in China.

Methods

This study was conducted from September 2016 to September 2018 in three Chinese urban hospitals. The results from the Xpert CT/NG test were compared to those from the Roche cobas^® 4800 CT/NG test. Discordant results were confirmed by DNA sequence analysis.

Results

In this study, 619 first void urine (FVU) specimens and 1,042 cervical swab specimens were included in the final dataset. There were no statistical differences between the results of the two tests for the detection of CT/NG in urine samples (p > 0.05), while a statistical difference was found in cervical swabs (p < 0.05). For CT detection, the sensitivity and specificity of the Xpert test were 100.0% (95%CI = 96.8-99.9) and 98.3% (95%CI = 96.6-99.2) for urine samples and 99.4% (95%CI = 96.5-100.0) and 98.6% (95%CI 97.5-99.2) for cervical swabs, respectively. For NG detection, the sensitivity and specificity of the Xpert test were 99.2% (95%CI = 94.9-100.0) and 100.0% (95%CI = 99.0-100.0) for urine and 100% (95%CI = 92.8-100.0) and 99.7% (95%CI = 99.0-99.9) for cervical swabs, respectively.

Conclusion

The Xpert CT/NG test exhibited high sensitivity and specificity in the detection of CT and NG in both urine and cervical samples when compared to the reference results. The 90-min turnaround time for CT and NG detection at the point of care using Xpert may enable patients to receive treatment promptly.

Pooled 3-Anatomic-Site Testing for Chlamydia trachomatis and Neisseria gonorrhoeae: A Systematic Review and Meta-Analysis

BACKGROUND

Pooled testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) may be a cost-saving solution to increase screening by simplifying testing procedures and reducing resource burdens. We conducted a systematic review and meta-analysis to examine the performance of pooled 3-anatomic-site testing (pharyngeal, rectal, and urogenital sites) for CT and NG in comparison with single-anatomic-site testing.

METHODS

We conducted a systematic literature search in PubMed, Embase, and Web of Science to identify original evaluation studies of the performance of pooled testing for CT and NG infections and identified 14 studies for inclusion. Each study was systematically evaluated for bias. We conducted bivariate fixed-effects and random-effects meta-analyses using a full Bayesian method of the positive percent agreement and negative percent agreement.

RESULTS

The combined positive percent agreement for CT was 93.11% (95% confidence interval [CI], 91.51%-94.55%), and the negative percent agreement was 99.44% (95% CI, 99.18%-99.65%). For NG, the combined positive percent agreement was 93.80% (95% CI, 90.26%-96.61%), and the negative percent agreement was 99.73% (95% CI, 99.30%-99.97%).

CONCLUSIONS

We found that pooled 3-anatomic-site tests performed similarly to single-anatomic-site tests for the detection of CT and NG. The pooled 3-anatomic-site tests have the added potential benefit of reduced cost and resource requirement, which could lead to improved testing access and screening uptake.

Diagnostic accuracy of pooling urine, anorectal, and oropharyngeal specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae: a systematic review and meta-analysis

BACKGROUND

Screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) at genital and extragenital sites is needed for most key populations, but molecular diagnostic tests for CT/NG are costly. We aimed to determine the accuracy of pooled samples from multiple anatomic sites from one individual to detect CT/NG using the testing of a single sample from one anatomic site as the reference.

METHODS

In this systematic review and meta-analysis, we searched five databases for articles published from January 1, 2000, to February 4, 2021. Studies were included if they contained original data describing the diagnostic accuracy of pooled testing compared with single samples, resource use, benefits and harms of pooling, acceptability, and impact on health equity. We present the pooled sensitivities and specificities for CT and NG using a bivariate mixed-effects logistic regression model. The study protocol is registered in PROSPERO, an international database of prospectively registered systematic reviews (CRD42021240793). We used GRADE to evaluate the quality of evidence.

RESULTS

Our search yielded 7814 studies, with 17 eligible studies included in our review. Most studies were conducted in high-income countries (82.6%, 14/17) and focused on men who have sex with men (70.6%, 12/17). Fourteen studies provided 15 estimates for the meta-analysis for CT with data from 5891 individuals. The pooled sensitivity for multisite pooling for CT was 93.1% [95% confidence intervals (CI) 90.5-95.0], I²=43.3, and pooled specificity was 99.4% [99.0-99.6], I²=52.9. Thirteen studies provided 14 estimates for the meta-analysis for NG with data from 6565 individuals. The pooled sensitivity for multisite pooling for NG was 94.1% [95% CI 90.9-96.3], I²=68.4, and pooled specificity was 99.6% [99.1-99.8], I²=83.6. Studies report significant cost savings (by two thirds to a third).

CONCLUSION

Multisite pooled testing is a promising approach to improve testing coverage for CT/NG in resource-constrained settings with a small compromise in sensitivity but with a potential for significant cost savings.

Swab-Yourself Trial With Economic Monitoring and Testing for Infections Collectively (SYSTEMATIC): Part 2. A Diagnostic Accuracy and Cost-effectiveness Study Comparing Rectal, Pharyngeal, and Urogenital Samples Analyzed Individually, Versus as a Pooled Specimen, for the Diagnosis of Gonorrhea and Chlamydia

BACKGROUND

Sexual history does not accurately identify those with extragenital Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT), so universal extragenital sampling is recommended. Nucleic acid amplification tests (NAATs) are expensive. If urogenital, plus rectal and pharyngeal, samples are analyzed, the diagnostic cost is trebled. Pooling samples into 1 NAAT container would cost the same as urogenital samples alone. We compared clinician triple samples analyzed individually with self-taken pooled samples for diagnostic accuracy, and cost, in men who have sex with men (MSM) and females.

METHODS

This was a prospective, convenience sample in United Kingdom sexual health clinic. Randomized order of clinician and self-samples from pharynx, rectum, plus first-catch urine (FCU) in MSM and vulvovaginal swabs (VVS) in females, for NG and CT detection.

RESULTS

Of 1793 participants (1284 females, 509 MSM), 116 had NG detected (75 urogenital, 83 rectum, 72 pharynx); 276 had CT detected (217 urogenital, 249 rectum, 63 pharynx). There was no difference in sensitivities between clinician triple samples and self-pooled specimens for NG (99.1% and 98.3%), but clinician samples analyzed individually identified 3% more chlamydia infections than pooled (99.3% and 96.0%; P = .027). However, pooled specimens identified more infections than VVS/FCU alone. Pooled specimens missed 2 NG and 11 CT infections, whereas VVS/FCU missed 41 NG and 58 CT infections. Self-taken pooled specimens were the most cost-effective.

CONCLUSIONS

FCU/VVS testing alone missed many infections. Self-taken pooled samples were as sensitive as clinician triple samples for identifying NG, but clinician samples analyzed individually identified 3% more CT infections than pooled. The extragenital sampling was achievable at no additional diagnostic cost to the FCU/VVS.

CLINICAL TRIALS REGISTRATION

NCT02371109.

The Performance of Pooled 3 Anatomic Site Testing for Chlamydia trachomatis and Neisseria gonorrhoeae Among Men Who Have Sex With Men and Transgender Women

BACKGROUND

Although molecular testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) is highly sensitive, the cost can be prohibitive. Those high costs are amplified when the recommended screening approach is used, which requires separate testing of specimens from 3 anatomic sites (rectal, pharyngeal and urogenital). Although individual molecular testing is standard of care, pooled testing may offer a cost-saving alternative.

METHODS

Using the Xpert® CT/NG assay (Cepheid, Sunnyvale, CA) we tested urine, rectal and pharyngeal swabs for CT and NG in a high-risk cohort of participants assigned male at birth who reported sex with other persons who were assigned male at birth. Remnant specimens (0.34 mL from each anatomic site) were combined to perform a single 'pooled' test. We calculated positive and negative percent agreement between the pooled testing results with standard of care Xpert CT/NG test results as the reference.

RESULTS

We conducted 644 pooled tests. Of those, 598 (92.3%) gave CT and NG results. The CT-positive and -negative percent agreement were 90.1% (95% confidence interval [CI], 80.7-95.9%) and 99.2% (98.1-99.8%), respectively. The NG-positive and -negative percent agreement were 96.2% (95% CI, 86.8-99.5%) and 99.8% (95% CI, 99.0-100%), respectively. Pooled testing identified 4 CT and 1 NG infections that were negative at all anatomic sites by individual testing.

CONCLUSIONS

Three-site pooled CT and NG testing performs similarly to single anatomic site testing among tests providing a valid result. Future cost analyses should evaluate the cost effectiveness of pooled 3-site testing to determine if such a strategy improves the feasibility and accessibility of molecular sexually transmitted infection testing.

To Pool or Not to Pool Samples for Sexually Transmitted Infections Detection in Men Who Have Sex With Men? An Evaluation of a New Pooling Method Using the GeneXpert Instrument in West Africa

BACKGROUND

Men who have sex with men (MSM) using preexposure prophylaxis (PrEP) are at risk for sexually transmitted infections (STIs). Therefore, PrEP services should include regular screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) at urethra, anorectum, and pharynx. However, financial and logistic challenges arise in low-resource settings. We assessed a new STI sample pooling method using the GeneXpert instrument among MSM initiating PrEP in West Africa.

METHODS

Urine, anorectal, and pharyngeal samples were pooled per individual for analysis. In case of an invalid result only (strategy 1) or a positive result of the pool (strategy 2), samples were analyzed individually to identify the infection's biological location. The results of 2 different pooling strategies were compared against the individual results obtained by a criterion standard.

RESULTS

We found a prevalence of 14.5% for chlamydia and 11.5% for gonorrhea, with a predominance of infections being extragenital (77.6%). The majority of infections were asymptomatic (88.2%). The pooling strategy 1, had a sensitivity, specificity and agreement for CT of 95.4%, 98.7%, and 0.93, respectively; and 92.3%, 99.2%, and 0.93 for pooling strategy 2. For NG, these figures were 88.9%, 97.7%, and 0.85 for strategy 1, and 88.9%, 96.7%, and 0.81 for strategy 2.

CONCLUSIONS

West African MSM have a high prevalence of extragenital and asymptomatic STIs. The GeneXpert method provides an opportunity to move from syndromic toward etiological STI diagnosis in low-income countries, as the platform is available in African countries for tuberculosis testing. Pooling will reduce costs of triple site testing.

Modified self-obtained pooled sampling to screen for Chlamydia trachomatis and Neisseria gonorrhoeae infections in men who have sex with men

OBJECTIVES

To assess whether pooled sample testing with nucleic acid amplification tests was a potential alternative to three single-site sample testing to screen for Chlamydia trachomatis and Neisseria gonorrhoeae infections in asymptomatic men who have sex with men.

METHODS

We prospectively compared pooled sample testing with single-site sample testing in asymptomatic MSM. Self-obtained paired rectal samples, one gargle sample and one first-void urine sample were collected from participants to generate two sets of samples: one for pooled sample testing and the other for single-site testing. We used modified pooled sampling, which is defined as the use of gargle samples, instead of swabs, for the pooled sample to test for pharyngeal infection.

RESULTS

This study included 513 MSM. The positive rates of C. trachomatis and N. gonorrhoeae were 20.3% and 11.7%, respectively, for single-site sample testing. Compared with the sensitivity of single-site testing as the gold standard, the sensitivities of pooled sample testing for C. trachomatis and N. gonorrhoeae were 94.2% (95% CI 88.0% to 97.3%) and 98.3% (95% CI 90.9% to 99.9%), respectively. The concordance rate and kappa coefficient were 98.3% (95% CI 96.7% to 99.2%) and 0.945 (95% CI 0.859 to 1.000), respectively, for C. trachomatis and 98.8% (95% CI 90.1% to 100%) and 0.943 (95% CI 0.857 to 1.000), respectively, for N. gonorrhoeae.

CONCLUSIONS

The modified pooled sampling had a comparably high consistency with single-site sample testing. The results strongly suggest that the gargle sample is suitable as a part of pooled sample for STI screening of C. trachomatis and N. gonorrhoeae.

Clinician-collected urethra swab: A good alternative sample type using cobas 4800 system for Chlamydia trachomatis and Neisseria gonorrhoeae in men

Background

Nucleic acid amplification tests (NAATs) are being used increasing to detection of CT (Chlamydia trachomatis) and NG (Neisseria gonorrhoeae) infections for superior sensitivity and specificity than other tests. Male first‐void urine (FVU) sample is the optimal sample type for detection of CT and NG by NAATs. Although not being the recommended by NAATs, clinician‐collected urethra swab (CCUS) is perhaps a good alternative sample type compared with the FVU sample in men.

Methods

Paired samples (FVU and CCUS) from one hundred male outpatients were simultaneously detected by urine pattern and swab pattern using cobas 4800 CT/NG assay on cobas 4800 system for the detection of CT and NG, respectively. And twenty‐one positive controls were also detected on cobas 4800 system.

Results

The CT/NG cycle thresholds (Ct) value of urine pattern is lower than that of swab pattern for the same positive samples (clinical samples and positive controls) on the cobas 4800 CT/NG assay. The final CT/NG results of two sample patterns from patients were highly consistent except for four discordant results.

Conclusion

CCUS is validated for a good alternative sample type for the CT/NG detection on the cobas 4800 system in this study.

A Population-Specific Optimized GeneXpert Pooling Algorithm for Chlamydia trachomatis and Neisseria gonorrhoeae To Reduce Cost of Molecular Sexually Transmitted Infection Screening in Resource-Limited Settings

The sexually transmitted infections (STIs) chlamydia (CT) and gonorrhea (NG) are often asymptomatic in women and undetected by syndromic management, leading to complications such as pelvic inflammatory disease, infertility, and ectopic pregnancy. Molecular testing, such as the GeneXpert CT/NG assay, is highly sensitive, but cost restraints preclude implementation of these technologies in resource-limited settings. Pooled testing is one strategy to reduce the cost per sample, but the extent of savings depends on disease prevalence. The current study describes a pooling strategy based on identification of sociodemographic and laboratory factors associated with CT/NG prevalence in a high-risk cohort of Zambian female sex workers and single mothers conducted from 2016 to 2019. Factors associated with testing positive for CT/NG via logistic regression modeling included city, younger age, lower education, long-acting reversible contraception usage, Trichomonas vaginalis infection, bacterial vaginosis, and incident syphilis infection. Based on these factors, the study population was stratified into high-, intermediate-, and low-prevalence subgroups and tested accordingly-individually, pools of 3, or pools of 4, respectively. The cost per sample was reduced from $18 to as low as $9.43 in the low-prevalence subgroup. The checklist tool and pooling approach described can be used in a variety of treatment algorithms to lower the cost per sample and increase access to molecular STI screening. This is particularly valuable in resource-limited settings to detect and treat asymptomatic CT/NG infections missed by traditional syndromic management.

Point-by-Point Progress: Gonorrhea Point of Care Tests

INTRODUCTION

Point-of-care (POC) tests for Neisseria gonorrhoeae (Ng) are urgently needed to control the gonorrhea epidemic, so patients can receive immediate diagnoses and treatment. While the advent of nucleic acid amplification tests (NAATs) has improved the accuracy of Ng identification, very few POC assays are able to provide results of such tests at the clinical visit. Additionally, antimicrobial resistance (AMR) presents a unique treatment challenge for Ng.

AREAS COVERED

This review notes that older POC tests have lower sensitivity for Ng, compared to the currently-available NAATs, and are not adequate for the current demand for high sensitivity. Promising newer assays, which can be used at the POC are covered. This review also includes data about clinicians' and patients' acceptability and expectations of POC tests for Ng, testing of extragenital specimens, pooling studies, as well as their impact clinically, and use in low-resource settings.

EXPERT OPINION

The ability to use POC tests to identify and immediately treat Ng infections at the patient encounter offers many benefits and opportunities. POC tests for Ng are currently available, but not widely used especially in low-resource settings. Further development of POC tests with AMR testing capacity is needed to help guide antimicrobial stewardship.

To pool or not to pool? Screening of Chlamydia trachomatis and Neisseria gonorrhoeae in female sex workers: pooled versus single-site testing

OBJECTIVES

As Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the most commonly reported STIs in Belgium and the majority of women infected are asymptomatic, targeted screening of patients in specified risk groups is indicated. To prevent long-term complications and interrupt transmission, extragenital samples should be included. As this comes with a substantial extra cost, analysis of a pooled sample from vaginal and extragenital sites could be a solution. In this study, we evaluated the feasibility of molecular testing for CT and NG in pooled versus single-site samples in a large cohort of female sex workers.

METHODS

Women were sampled from three anatomical sites: a pharyngeal, a vaginal and a rectal swab. Each sample was vortexed, and 400 µL of transport medium from each sample site was pooled into an empty tube. NAAT was performed using the Abbott RealTime CT/NG assay on the m2000sp/rt system.

RESULTS

We included 489 patients: 5.1% were positive for CT; 2.0% were positive for NG and 1.4% were coinfected, resulting in an overall prevalence of 6.5% (95% CI 4.5% to 9.1%) for CT and 3.5% (95% CI 2.0% to 5.5%) for NG. From the 42 patients positive on at least one non-pooled sample, only 5 gave a negative result on the pooled sample, resulting in a sensitivity of 94% (95% CI 79% to 99%) for CT and 82% (95% CI 57% to 96%) for NG. The missed pooled samples were all derived from single-site infections with low bacterial loads. The possibility of inadequate self-sampling as a cause of false negativity was excluded, as 4/5 were collected by the physician. Testing only vaginal samples would have led to missing 40% of CT infections and 60% of NG infections.

CONCLUSIONS

Pooling of samples is a cost-saving strategy for the detection of CT and NG in women, with minimal decrease in sensitivity. By reducing costs, more patients and more extragenital samples can be tested, resulting in higher detection rates.

Pooling Pharyngeal, Anorectal, and Urogenital Samples for Screening Asymptomatic Men Who Have Sex with Men for Chlamydia trachomatis and Neisseria gonorrhoeae

Screening for Chlamydia trachomatis and Neisseria gonorrhoeae at the pharyngeal, urogenital, and anorectal sites is recommended for men who have sex with men (MSM). Combining the three individual-site samples into a single pooled sample could result in significant cost savings, provided there is no significant sensitivity reduction. The aim of this study was to examine the sensitivity of pooled samples for detecting chlamydia and gonorrhea in asymptomatic MSM using a nucleic acid amplification test. Asymptomatic MSM who tested positive for chlamydia or gonorrhoea were invited to participate. Paired samples were obtained from participants prior to administration of treatment. To form the pooled sample, the anorectal swab was agitated in the urine specimen transport tube and then discarded. The pharyngeal swab and 2 ml of urine sample were then added to the tube. The difference in sensitivity between testing of pooled samples and individual-site testing was calculated against an expanded gold standard, where an individual is considered positive if either pooled-sample or individual-site testing returns a positive result. All samples were tested using the Aptima Combo 2 assay. A total of 162 MSM were enrolled in the study. Sensitivities of pooled-sample testing were 86% (94/109; 95% confidence interval [CI], 79 to 92%]) for chlamydia and 91% (73/80; 95% CI, 83 to 96%) for gonorrhea. The sensitivity reduction was significant for chlamydia (P = 0.02) but not for gonorrhea (P = 0.34). Pooling caused 22 infections (15 chlamydia and 7 gonorrhoea) to be missed, and the majority were single-site infections (19/22). Pooling urogenital and extragenital samples from asymptomatic MSM reduced the sensitivity of detection by approximately 10% for chlamydia but not for gonorrhea.

Reduced sensitivity from pooled urine, pharyngeal and rectal specimens when using a molecular assay for the detection of chlamydia and gonorrhoea near the point of care

Background The aim of this study was to compare the performance of pooled self-collected urogenital, pharyngeal and anorectal specimens to that of individual specimen results for the molecular detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) near the point of care (POC) for diagnostic sensitivity.

METHODS

Clients (mostly men who have sex with men) attending an urban community testing service and three sex-on-premises venues in Brisbane, Australia, were offered CT and NG testing by trained lay providers. Participants provided three self-collected specimens (urine, pharyngeal and rectal) for testing by GeneXpert (Cepheid, Sunnyvale, CA, USA). If any of the individual specimens from a participant were positive, all three specimens were pooled and retested.

RESULTS

Of the 388 participants who provided three individual anatomical specimens, 76 (19.6%) were found to be positive for CT and/or NG at one or more sites. The pooling approach failed to detect five CT rectal and four NG pharyngeal infections. The overall performance (sensitivity) of the pooling approach compared with individual specimen testing and Cohen's κ were 90.0% and 0.86 respectively for CT and 89.7% and 0.89 respectively for NG.

CONCLUSIONS

Reduced sensitivity was observed when using pooled specimens for the detection of CT and NG using GeneXpert near the POC, similar to results reported in laboratory-based CT and NG pooling studies. These data suggest specimen pooling is feasible near to the POC, potentially saving time and costs when screening at-risk populations for CT and NG. Our data also suggest a reduction in pooled urine could improve overall test sensitivity.

Peer-delivered point-of-care testing for Chlamydia trachomatis and Neisseria gonorrhoeae within an urban community setting: a cross-sectional analysis

Background The advent of fully automated nucleic acid amplification test (NAAT) technology brings new public health opportunities to provide Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) point-of-care testing (POCT) in non-traditional settings.

METHODS

This pilot study evaluated the integration of the CT/NG Xpert diagnostic assay into an urban peer-led community setting providing HIV and syphilis POCT. A comprehensive protocol of testing, result notification, referral and follow up, managed by peer test facilitators, was undertaken.

RESULTS

Over 67 weeks, there were 4523 occasions of CT/NG testing using urine, oropharyngeal and anorectal samples with 25.7% (803) of the 3123 unique participants returning for repeat testing. The prevalence of CT and NG was 9.5% and 5.4% respectively. Where CT and or NG infection was detected, 98.4% (604/614) of participants were successfully notified of detected infection and referred for treatment. Evaluation Survey responses (11.4%, 516/4523) indicated a substantial proportion of respondents (27.1%, 140/516) 'would not have tested anywhere else'. Of note, 17.8% (92/516) of participants reported no previous CT/NG test and an additional 17.8% (92/516) reported testing more than 12 months ago. A total of 95.9% (495/516) of participants 'Strongly agreed' or 'Agreed' to being satisfied with the service.

CONCLUSION

The project successfully demonstrated an acceptable and feasible model for a peer-delivered community-led service to provide targeted molecular CT/NG POCT. This model offers capacity to move beyond the traditional pathology and STI testing services and establish community-led models that build trust and increase testing rates for key populations of epidemiological significance.

Meta-analysis of the Cepheid Xpert® CT/NG assay for extragenital detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections

Background Most studies evaluating extragenital testing performance for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) detection by the Xpert® CT/NG show high per cent agreement with comparison assays; however, the precision around positive per cent agreement is low and thus the values that have been reported are not highly informative. Therefore, a systematic review was conducted and data from five studies were combined to better assess positive per cent agreement.

METHODS

The literature indexed on PubMed.gov was searched. Included studies were those that were an evaluation of the Xpert CT/NG assay with rectal and/or pharyngeal specimen types compared with another nucleic acid amplification test (NAAT), the Aptima transcription mediated amplification assay. A full Bayesian method was used for bivariate fixed-effect meta-analysis of positive and negative per cent agreement and pooled estimates (and 95% confidence intervals (CI)) were presented for each.

RESULTS

The pooled positive and negative per cent agreement for detection of CT in rectal specimens was 89.72% (95% CI: 84.97%, 93.64%) and 99.23% (95% CI: 98.74%, 99.60%), and in pharyngeal specimens, they were 89.96% (95% CI: 66.38%, 99.72%) and 99.62% (95% CI: 98.95%, 99.95%) respectively. For NG detection in rectal specimens, the pooled positive and negative per cent agreement was 92.75% (95% CI: 87.91%, 96.46%) and 99.75% (95% CI: 99.46%, 99.93%), and in pharyngeal specimens, they were 92.51% (95% CI: 85.84%, 97.18%) and 98.56% (95% CI: 97.69%, 99.23%) respectively.

CONCLUSIONS

It was found that the Xpert CT/NG assay performed similarly to the Aptima transcription mediated amplification assay for the detection of CT and NG in extragenital specimens. The Xpert assay has the benefit of providing faster results at the point-of-care, thus reducing the turnaround time for results, potentially enabling same-day treatment.

Molecular point-of-care testing for chlamydia and gonorrhoea in Indigenous Australians attending remote primary health services (TTANGO): a cluster-randomised, controlled, crossover trial

BACKGROUND

Timely diagnosis and treatment of sexually transmissible infections will prevent morbidity and onward transmission. We aimed to assess the efficacy of a point-of-care molecular test for Chlamydia trachomatis and Neisseria gonorrhoeae infections at the cluster level to improve infection management among Indigenous Australian communities with high prevalence of sexually transmissible infections.

METHODS

In this cluster-randomised crossover study, we recruited primary health services in Western Australia, Far North Queensland, and South Australia that provide care to Indigenous people in regional or remote locations. The services were eligible if they did 150 or more tests for C trachomatis or N gonorrhoeae infection per year among individuals aged 16-29 years, and if C trachomatis or N gonorrhoeae positivity was 10% or higher. Services were randomly assigned (1:1) by use of a random-number generator, stratified by geographical region, to either standard care conditions with routine laboratory-based sexually transmissible infection testing for 12 months followed by 12 months of intervention with molecular point-of-care testing, or the reverse sequence. The primary outcome was the proportion of people (aged 16-29 years) found to have C trachomatis or N gonorrhoeae who had a positive result at retesting 3 weeks to 3 months after treatment, and a secondary outcome was treatment within 7 days, both in those aged 16-29 years and at the cluster level. We did these analyses using data from all participants who had a positive result at testing, by point-of-care of laboratory testing (ie, the intention-to-treat population). The trial is registered with Australian and New Zealand Clinical Trials Registry (ACTRN12613000808741).

FINDINGS

Between June 1, 2013, and Feb 29, 2016, 12 health services were enrolled and randomly assigned to standard care followed by intervention (six) and the reverse sequence (six). After randomisation, one health service that was initially assigned to standard care was excluded because it no longer met the inclusion criteria. 455 individuals tested positive for C trachomatis or N gonorrhoeae infection in the intervention group, and 405 tested positive in the standard care group. In the intervention group, 12 (19%) of 63 individuals retested had a positive test result, compared with nine (13%) of 67 with positive retests in the standard care group (relative ratio [RR] 1·42, 95% CI 0·64-3·13; p=0·405), and 347 (76%) were treated within 7 days in the intervention group, compared with 191 (47%) in the standard care group (RR 1·66, 1·41-1·93; p<0·0001).

INTERPRETATION

Retesting rates were too low to draw conclusions on the effect of the intervention on repeat infections. Further research will be needed to determine whether point-of-care tests have an effect on reinfection rates, and the sustainability of using this technology. However, our findings show that time to treatment of C trachomatis or N gonorrhoeae infections in primary care clinics in remote areas in Australia with a high prevalence of sexually transmissible infections could be substantially reduced by the use of molecular point-of-care tests.

FUNDING

The National Health and Medical Research Council, Australia.

Correlations of chlamydia and gonorrhoea among pharyngeal, rectal and urethral sites among Thai men who have sex with men: multicentre community-led test and treat cohort in Thailand

OBJECTIVE

Routine screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections in sexually exposed anatomical sites may be challenging in resource-limited settings. The objective of this study was to determine the proportion of missed CT/NG diagnoses if a single anatomical site screening was performed among men who have sex with men (MSM) by examining the pattern of anatomical sites of CT/NG infections.

METHODS

Thai MSM were enrolled to the community-led test and treat cohort. Screening for CT/NG infections was performed from pharyngeal swab, rectal swab and urine using nucleic acid amplification testing. The correlations of CT/NG among the three anatomical sites were analysed.

RESULTS

Among 1610 MSM included in the analysis, 21.7% had CT and 15.5% had NG infection at any anatomical site. Among those tested negative for CT or NG infection at either pharyngeal, rectal or urethral site, 8%-19% had CT infection and 7%-12% had NG infection at the remaining two sites. Of the total 349 CT infections, 85.9%, 30.6% and 67.8% would have been missed if only pharyngeal, rectal or urethral screening was performed, respectively. Of the total 249 NG infection, 55.7%, 39.6% and 77.4% would have been missed if only pharyngeal, rectal or urethral screening was performed, respectively. The majority of each anatomical site of CT/NG infection was isolated to their respective site, with rectal site having the highest proportion of isolation: 78.9% of rectal CT and 62.7% of rectal NG infection.

CONCLUSIONS

A high proportion of CT/NG infections would be missed if single anatomical site screening was performed among MSM. All-site screening is highly recommended, but if not feasible, rectal screening provides the highest yield of CT/NG diagnoses. Effort in lowering the cost of the CT/NG screening test or developing affordable molecular technologies for CT/NG detection is needed for MSM in resource-limited settings.

TRIAL REGISTRATION NUMBER

NCT03580512; Results.

Factors That Influence Confirmation of Neisseria gonorrhoeae Positivity by Molecular Methods

Several Neisseria gonorrhoeae nucleic acid amplification tests (NAATs) with high sensitivity exist. However, the specificity of N. gonorrhoeae NAATs may be suboptimal, particularly for extragenital biospecimens. Consequently, confirmation with a second NAAT is common, although this represents a burden on resources. Furthermore, the rationale for confirmation is contentious. The objective of this work was to assess N. gonorrhoeae confirmation in over 13,000 N. gonorrhoeae screen-positive samples representing various biospecimens and three separate screening assays, the Abbott RealTime CT/NG (Abbott Molecular, Inc., Des Plaines, IL), the Cobas CT/NG test (Roche Molecular Systems Inc., Alameda, CA), and the BD ProbeTec ET CT/GC amplified DNA assay (BD Diagnostics, Sparks, MD). Factors predictive of confirmation were determined via logistic regression involving sex, year, whether the sample was formally validated, and sample site. Level of confirmation varied according to screening assay (96.2%, 86.0%, and 73.9% for the Abbott, Roche, and BD tests, respectively) in sample types formally included according to the manufacturers' instructions (i.e., validated). Sex did not affect confirmation for 2/3 assays, and the likelihood of confirmation of samples not formally included in manufacturer instructions (i.e., nonvalidated) was 89.1%, 82.1%, and 59.2% for the Abbott, Roche, and BD tests, respectively. Rectal swabs, which are nonvalidated samples, confirmed in 91.5%, 90.1%, and 87.4% of samples initially tested with the respective assays. The requirement to confirm N. gonorrhoeae in validated samples is not required for all NAATs, although initial assay-specific evaluation is justified given observed variability. Rectal samples represent robust biospecimens for N. gonorrhoeae NAAT testing and may not require confirmation when screened with the assays described.

WHO laboratory validation of Xpert® CT/NG and Xpert® TV on the GeneXpert system verifies high performances

Effective tests for diagnosis of sexually transmitted infections (STIs), used point of care to inform treatment and management decisions, are urgently needed. We evaluated the analytical sensitivity and specificity of the Xpert^® CT/NG and Xpert^® TV tests, examining 339 samples spiked with phenotypically and/or genetically diverse strains of Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis, and other related species that may cross-react. The APTIMA Combo 2 test and APTIMA TV test were used as reference tests. The analytical sensitivity for all three agents in the Xpert^® CT/NG and Xpert^® TV tests was ≤10² genome equivalents/reaction. The analytical specificity of both tests was high. False-positive results were identified in the Xpert^® TV test when challenging with high concentrations of Trichomonas tenax, Trichomonas gallinae, Trichomonas stableri, and Trichomonas aotus. However, the clinical relevance of these cross-reactions can likely be neglected, because these species have not been identified in urogenital samples from humans. In conclusion, the analytical sensitivity and specificity of the user-friendly Xpert^® CT/NG and Xpert^® TV tests on the GeneXpert system were high. The results support the use of specimens from also extra-genital sites, for example, pharynx and rectum. However, appropriate clinical validations are additionally required.

Evaluation of a Hydrogel-Based Diagnostic Approach for the Point-of-Care Based Detection of Neisseria gonorrhoeae

Eleven primer pairs were developed for the identification of Neisseria gonorrhoeae. The sensitivity and specificity of these primers were evaluated by Real Time (RT)-PCR melt curve analyses with DNA from 145 N. gonorrhoeae isolates and 40 other Neisseria or non-Neisseria species. Three primer pairs were further evaluated in a hydrogel-based RT-PCR detection platform, using DNA extracted from 50 N. gonorrhoeae cultures. We observed 100% sensitivity and specificity in the hydrogel assay, confirming its potential as a point-of-care test (POCT) for N. gonorrhoeae diagnosis.

Molecular test for chlamydia and gonorrhoea used at point of care in remote primary healthcare settings: a diagnostic test evaluation

OBJECTIVES

A new molecular test for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) (GeneXpert CT/NG) has been demonstrated to be as accurate as conventional nucleic acid amplification tests (NAAT), but performance has not been evaluated in routine primary care, performed at the point of care by clinicians. We aimed to examine its diagnostic performance when used by clinicians in remote community health services in Australia with high prevalences of CT and NG infection. The trial was registered with the Australian and New Zealand Clinical Trials Registry (#12613000808741) METHODS: At 12 health services, training was provided to 99 clinicians in the use of the GeneXpert CT/NG assay who tested specimens from all patients undergoing STI screening. Specimens were also sent in parallel for conventional laboratory-based NAATs and the concordance of results was evaluated.

RESULTS

Clinicians conducted 2486 tests: CT concordance was 99.4% (95% CI 99.1 to 99.7) with a positive concordance of 98.6% (95% CI 95.9 to 99.7) and negative concordance of 99.5% (95% CI 99.1 to 99.8); NG concordance was 99.9% (95% CI 99.7 to 100.0) with a positive concordance of 100.0% (95% CI 97.5 to 100.0) and negative concordance of 99.9% (95% CI 99.7 to 100.0).

CONCLUSIONS

In this first study reporting routine point-of-care use of GeneXpert CT/NG by primary care clinicians, we found excellent concordance with conventional NAATs. The use of the GeneXpert CT/NG at the point of care could potentially transform management and control of these infections in many endemic settings, including low/middle-income countries.

Syphilis incidence in men who have sex with men with human immunodeficiency virus comorbidity and the importance of integrating sexually transmitted infection prevention into HIV care

INTRODUCTION

Syphilis continues to be a growing epidemic among men who have sex with men (MSM), particularly for those living with the human immunodeficiency virus (HIV). In 2016, MSM accounted for 80% of primary and secondary syphilis diagnoses in men in the United States; almost half of who were also HIV-infected. The synergistic relationship between HIV and syphilis has significant implications not only for HIV patient management, but also for sexually transmitted infection (STI) control among MSM. Areas covered: We review the literature on STI screening and treatment barriers at the patient-, provider-, and health system-levels, and present strategies to incorporate STI prevention into HIV care settings. Expert commentary: Integration of STI prevention into HIV care is paramount to stop the epidemic of not only syphilis, but also other curable STIs like gonorrhea and chlamydia. Although guidelines have been established for STI testing in HIV-infected MSM, screening rates continue to be lower than desired. Gonorrhea and chlamydia screening is below 50% in HIV-infected MSM; interventions that improve testing of those two infections must be implemented. For syphilis control, other additional strategies such as chemoprophylaxis should be considered given syphilis screening is above 50% in HIV-infected MSM.