Can mailed swab samples be dry-shipped for the detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis by nucleic acid amplification tests?

The impact of COVID-19 pandemic on technologic and process innovation in point-of-care diagnostics for sexually transmitted infections

The STI diagnostic landscape of FDA cleared tests for use at point-of-care (POC), as well as those emergency use authorized for COVID-19 are reviewed; some of these COVID-19 diagnostics may have platform potential as STI diagnostics. Finally, process innovation is described with self-collection and hub-and-spoke mail-in to reference lab models. Movement of Clinical Laboratory Improvement Amendments (CLIA)-waived POC tests to over-the-counter formats will make tests more accessible to consumers. Together with public health messaging, these measures could accelerate STI and COVID-19 syndemic diagnostic solutions.

Landscape Review of Mail-in Self-Collection, Programs for Sexually Transmitted Infections

BACKGROUND

Mail-in self-collection of samples with centralized reference laboratory sexually transmitted infection (STI) testing has been shown to be feasible with equivalent performance. Commercial, fee-for-service mail-in testing Web sites seem to be popular. These sites are currently unregulated by the US Food and Drug Administration.

METHODS

To compile a list of US organizations offering mail-in testing for STIs/HIV, the phrases "mail-in STI testing" and "home STI testing" were entered into search engines. Supplementary information was collected by organization email or "Contact Us" submission.

RESULTS

Information was collected from 20 programs in the United States offering STI mail-in, self-collection testing services. Five programs (25%) were free to consumers. Six organizations (30%) only offered prefixed kits (STIs tested could not be selected). Half of the organizations provided extragenital testing, 2 (10%) did not provide extragenital testing, and the 8 others (40%) did not clarify. Three organizations (15%) used their own laboratory, 11 (55%) did not provide laboratory information. One commercial laboratory provided services to 5 organizations.

CONCLUSIONS

Mail-in self-collection services are ubiquitous and exist in all states except 2; STI testing public health programs that offer testing at no cost to the consumer are only in 46% of states. Mail-in testing is likely a permanent fixture in sexual health services and will be an important component of a hybrid approach that complements that of static clinic services.

Comparing mail-in self-collected specimens sent via United States Postal Service versus clinic-collected specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in extra-genital sites

Objectives

To evaluate the concordance between clinic-collected extra-genital specimens and self-collected mailed-in extra-genital specimens among participants seeking sexually transmitted infection testing at a free clinic in Hollywood, CA.

Methods

A convenience sample of 210 men who have sex with men were enrolled between February 29, 2016 and December 21, 2016 and received mail-in testing kits for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG). All testing was performed using the GeneXpert® CT/NG (Cepheid, Sunnyvale, CA).

Results

From the 210 mail-in kits distributed, 149 mail-in kits (71.0%) were returned to the laboratory, resulting in 145 pairs (clinic-collected and mail-in) of rectal test results and 148 pairs of pharyngeal test results for both CT and NG detection. The concordance was 95.0% for all CT rectal tests, 99.3% for all CT pharyngeal tests, 95.7% for all NG rectal tests, and 97.2% for all NG pharyngeal tests.

Conclusion

Roughly two-thirds of mail-in test kits were returned and concordance was generally high, however more than one-third of positive results were missed in mail-in samples. The prevalence of potential false-negative results among mail-in samples warrants caution when implementing mail-in STI testing strategies.

Comparison of the Cepheid GeneXpert CT/NG assay to the Hologic Aptima Combo2 assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in self-collected rectal swabs

Self-collected rectal-swabs were tested for CT and NG on GeneXpert CT/NG as compared to APTIMA Combo2. Of 448 rectal-swabs, 22 were positive for CT; 7 for NG on both assays; two were discordant. Sensitivity and specificity of GeneXpert was 95.5% and 99.7% for chlamydia, respectively; for gonorrhea both were 100%.

Reduced-cost Chlamydia trachomatis-specific multiplex real-time PCR diagnostic assay evaluated for ocular swabs and use by trachoma research programmes

INTRODUCTION

Trachoma, caused by the intracellular bacterium Chlamydia trachomatis (Ct), is the leading infectious cause of preventable blindness. Many commercial platforms are available that provide highly sensitive and specific detection of Ct DNA. However, the majority of these commercial platforms are inaccessible for population-level surveys in resource-limited settings typical to trachoma control programmes. We developed two low-cost quantitative PCR (qPCR) tests for Ct using readily available reagents on standard real-time thermocyclers.

METHODS

Each multiplex qPCR test targets one genomic and one plasmid Ct target in addition to an endogenous positive control for Homo sapiens DNA. The quantitative performance of the qPCR assays in clinical samples was determined by comparison to a previously evaluated droplet digital PCR (ddPCR) test. The diagnostic performance of the qPCR assays were evaluated against a commercial assay (artus C. trachomatis Plus RG PCR, Qiagen) using molecular diagnostics quality control standards and clinical samples. We examined the yield of Ct DNA prepared from five different DNA extraction kits and a cold chain-free dry-sample preservation method using swabs spiked with fixed concentrations of human and Ct DNA.

RESULTS

The qPCR assay was highly reproducible (Ct plasmid and genomic targets mean total coefficients of variance 41.5% and 48.3%, respectively). The assay detected 8/8 core specimens upon testing of a quality control panel and performed well in comparison to commercially marketed comparator test (sensitivity and specificity>90%). Optimal extraction and sample preservation methods for research applications were identified.

CONCLUSION

We describe a pipeline from collection to diagnosis providing the most efficient sample preservation and extraction with significant per test cost savings over a commercial qPCR diagnostic assay. The assay and its evaluation should allow control programs wishing to conduct independent research within the context of trachoma control, access to an affordable test with defined performance characteristics.

Stability Studies on Dry Swabs and Wet Mailed Swabs for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Aptima Assays

The Aptima Combo 2 (AC2) and Aptima CT (ACT) (Hologic Inc., San Diego, CA) are nucleic acid amplification tests (NAATs) that detect Chlamydia trachomatis AC2 also detects Neisseria gonorrhoeae Storage and temperature conditions may impact the utility of NAATs in some settings and screening programs. We evaluated specimen stability for use beyond the Aptima package insert specifications for temperature and duration of storage (between 2°C and 30°C and 60 days, respectively) in two studies: (i) dry C. trachomatis-seeded swabs were used with ACT after storage at 4°C, 23°C, or 36°C for up to 84 days and (ii) swabs seeded with C. trachomatis and N. gonorrhoeae and then placed in transport medium were tested with AC2, after being mailed via the U.S. Postal Service to three different sites. Prolonged storage of samples had no effect, and samples stored at 4°C, 23°C, and 36°C for up to 84 days yielded comparable ACT positivities, although there was a drop in signal intensity for virtually all specimens under all storage/shipping conditions after day 21. In the mailing study, 80%, 52% and 29% of seeded swabs were exposed to temperatures of >30°C during three rounds in transit, and 2% reached temperatures of >40°C. No evidence of signal degradation in the AC2 assay for detection of C. trachomatis or N. gonorrhoeae was observed, although some mailed swabs took more than 5 weeks to reach the laboratory site. These two studies support the potential use of swabs at temperatures above 36°C and storage beyond 60 days and provide confidence regarding this commercially available NAAT for testing of specimens after mailing.

Performance of self-collected penile-meatal swabs compared to clinician-collected urethral swabs for the detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, and Mycoplasma genitalium by nucleic acid amplification assays

Men were enrolled in a study to assess the performance and acceptability of self-collected penile meatal swabs as compared to clinician-collected urethral swabs for sexually transmitted infections (STIs). We expected penile-meatal swabs to perform favorably to urethral swabs for Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), and Mycoplasma genitalium (MG) detection by nucleic acid amplification assays (NAATs). Of 203 swab pairs tested; for CT, penile-meatal swab sensitivity was 96.8% and specificity was 98.8%. NG sensitivity and specificity were 100% and 98.9%, respectively. For TV, sensitivity was 85.0% and specificity was 96.7%. For MG sensitivity and specificity were 79.3% and 99.4%, respectively. No significant statistical differences between sample type accuracy (CT: P=0.625; NG: P=0.248; TV: P=0.344; and MG: P=0.070) existed. Most men, 90.1%, reported self-collection of penile-meatal swabs as "Very Easy" or "Easy". Self-collected penile-meatal swabs appeared acceptable for NAAT STI detection and an acceptable collection method by men.

Low Prevalence of Ocular Chlamydia trachomatis Infection and Active Trachoma in the Western Division of Fiji

Background

Trachoma is the leading infectious cause of blindness and is caused by ocular infection with the bacterium Chlamydia trachomatis (Ct). While the majority of the global disease burden is found in sub-Saharan Africa, the Western Pacific Region has been identified as trachoma endemic. Population surveys carried out throughout Fiji have shown an abundance of both clinically active trachoma and trachomatous trichiasis in all divisions. This finding is at odds with the clinical experience of local healthcare workers who do not consider trachoma to be highly prevalent. We aimed to determine whether conjunctival infection with Ct could be detected in one administrative division of Fiji.

Methods

A population-based survey of 2306 individuals was conducted using the Global Trachoma Mapping Project methodology. Population prevalence of active trachoma in children and trichiasis in adults was estimated using the World Health Organization simplified grading system. Conjunctival swabs were collected from 1009 children aged 1–9 years. DNA from swabs was tested for the presence of the Ct plasmid and human endogenous control.

Results

The prevalence of active trachoma in 1–9 year olds was 3.4%. The age-adjusted prevalence was 2.8% (95% CI: 1.4–4.3%). The unadjusted prevalence of ocular Ct infection in 1–9 year-olds was 1.9% (19/1009), and the age-adjusted infection prevalence was 2.3% (95% CI: 0.4–2.5%). The median DNA load was 41 Ct plasmid copies per swab (min 20, first quartile 32, mean 6665, third quartile 161, max 86354). There was no association between current infection and follicular trachoma. No cases of trachomatous trichiasis were identified.

Discussion

The Western Division of Fiji has a low prevalence of clinical trachoma. Ocular Ct infections were observed, but they were predominantly low load infections and were not correlated with clinical signs. Our study data suggest that trachoma does not meet the WHO definition of a public health problem in this Division of Fiji, but the inconsistency with previous studies warrants further investigation.

Trachoma, caused by ocular strains of Chlamydia trachomatis, represents a major global public health issue, and is the subject of an international elimination campaign. Until recently, data on trachoma in the Pacific Island states have been sparse. The most recent studies have conflicted in their estimates of trachomatous disease burden in Fiji, therefore, surveys using alternative markers (infection testing plus grading) to those already used (grading alone) are warranted to try to shed further light on trachoma epidemiology in this setting. We used an externally validated clinical assessment protocol to show that evidence of active trachoma is present at a low prevalence, and we did not find any cases of trichiasis, the sight-threatening stage of trachoma. From testing of conjunctival swabs with a validated, next-generation PCR, we also found that C. trachomatis was present at a low prevalence. Our clinical data suggest that trachoma does not meet the WHO definition of a public health problem in this Division of Fiji, but the inconsistency with previous studies warrants further investigation.

Evaluation of Presto(plus) assay and LightMix kit Trichomonas vaginalis assay for detection of Trichomonas vaginalis in dry vaginal swabs

This is an evaluation study of the Presto(plus) Assay for T. vaginalis by comparing to the TIB MOLBIOL LightMix Kit Trichomonas vaginalis Assay using 615 dry collected vaginal and rectal swabs. Discordant samples were analyzed by the Qiagen® Microbial DNA qPCR for TV Assay. Both assays showed comparable performances (McNemar p>0.05).

Opportunities and pitfalls of molecular testing for detecting sexually transmitted pathogens

In the last 20 years, nucleic acid amplification tests (NAATs) have gradually replaced traditional methods for the detection of sexually transmitted infections. NAAT technology comes with some considerable benefits for diagnosis, including increased sensitivity, rapid result turnaround and suitability for high throughput screening of asymptomatic individuals using more-readily available specimens. However, the transition to NAAT has not come without its problems. False-negative and false-positive results have been reported owing to various technical issues. Furthermore, increased reliance on NAATs for diagnosis have created the need to develop NAAT-based methods to inform treatment, being an area that presents its own set of challenges. In this review article, we explore NAAT-based detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis. In doing so, we consider the benefits and limitations of NAAT-based technology and highlight areas where further research and development is in need.

Background review for the '2015 European guideline on the management of Chlamydia trachomatis infections'

SummaryChlamydia trachomatis infections are major public health concerns globally. Of particular grave concern is that the majority of persons with anogenital Chlamydia trachomatis infections are asymptomatic and accordingly not aware of their infection, and this silent infection can subsequently result in severe reproductive tract complications and sequelae. The current review paper provides all background, evidence base and discussions for the 2015 European guideline on the management of Chlamydia trachomatis infections (Lanjouw E, et al. Int J STD AIDS 2015). Comprehensive information and recommendations are included regarding the diagnosis, treatment and prevention of anogenital, pharyngeal and conjunctival Chlamydia trachomatis infections in European countries. However, Chlamydia trachomatis also causes the eye infection trachoma, which is not a sexually transmitted infection. The 2015 European Chlamydia trachomatis guideline provides up-to-date guidance regarding broader indications for testing and treatment of Chlamydia trachomatis infections; clearer recommendation of using validated nucleic acid amplification tests only for diagnosis; advice on (repeated) Chlamydia trachomatis testing; recommendation of increased testing to reduce the incidence of pelvic inflammatory disease and prevent exposure to infection and recommendations to identify, verify and report Chlamydia trachomatis variants. Improvement of access to testing, test performance, diagnostics, antimicrobial treatment and follow-up of Chlamydia trachomatis patients are crucial to control its spread.

2015 European guideline on the management of Chlamydia trachomatis infections

Chlamydia trachomatis infections, which most frequently are asymptomatic, are major public health concerns globally. The 2015 European C. trachomatis guideline provides: up-to-date guidance regarding broader indications for testing and treatment of C. trachomatis infections; a clearer recommendation of using exclusively-validated nucleic acid amplification tests for diagnosis; advice on (repeated) C. trachomatis testing; the recommendation of increased testing to reduce the incidence of pelvic inflammatory disease and prevent exposure to infection; and recommendations to identify, verify and report C. trachomatis variants. Improvement of access to testing, test performance, diagnostics, antimicrobial treatment and follow-up of C. trachomatis patients are crucial to control its spread. For detailed background, evidence base and discussions, see the background review for the present 2015 European guideline on the management of Chlamydia trachomatis infections (Lanjouw E, et al. Int J STD AIDS. 2015).

2015 UK national guideline for the management of infection with Chlamydia trachomatis

This guideline offers recommendations on the diagnostic tests, treatment regimens and health promotion principles needed for the effective management of Chlamydia trachomatis genital infection. It covers the management of the initial presentation, as well the prevention of transmission and future infection. The guideline is aimed at individuals aged 16 years and older presenting to healthcare professionals working in departments offering Level 3 care in sexually transmitted infections management within the UK. However, the principles of the recommendations should be adopted across all levels, using local care pathways where appropriate.

Evaluation of pooled ocular and vaginal swabs by the Cepheid GeneXpert CT/NG assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae compared to the GenProbe Aptima Combo 2 Assay

Ocular swabs from Tanzania were tested for Chlamydia trachomatis (CT), and self-collected vaginal swabs collected through a home collection program, iwantthekit.org, were tested for Neisseria gonorrhoeae and CT to evaluate Cepheid GeneXpert for the use of pooling multiple specimens before testing. GeneXpert shows to be a promising test for pooling.

Paper-based molecular diagnostic for Chlamydia trachomatis

Herein we show the development of a minimally instrumented paper-based molecular diagnostic for point of care detection of sexually transmitted infections caused by Chlamydia trachomatis. This new diagnostic platform incorporates cell lysis, isothermal nucleic acid amplification, and lateral flow visual detection using only a pressure source and heat block, eliminating the need for expensive laboratory equipment. This paper-based test can be performed in less than one hour and has a clinically relevant limit of detection that is 100x more sensitive than current rapid immunoassays used for chlamydia diagnosis.

Advances in sampling and screening for chlamydia

Chlamydia is the most commonly diagnosed bacterial sexually transmitted infection in the developed world, with diagnosis rates continuing to increase each year. As chlamydia is largely asymptomatic, screening and treatment is the main way to detect cases and reduce transmission. Recent advances in self-collected specimens and laboratory tests has made chlamydia screening easier to implement as well as possible in nonclinical settings. This review will discuss new approaches to specimen collection and how these have expanded opportunities for reaching target populations for chlamydia screening. Furthermore, it will discuss how advanced molecular microbiological methods can be used with self-collected specimens to further our knowledge of the epidemiology of chlamydia and the dynamics of transmission.

Swabs (dry or collected in universal transport medium) and semen can be used for the detection of Chlamydia trachomatis using the cobas 4800 system

In this prospective study, the fully automated cobas 4800 CT/NG and the cobas TaqMan CT tests were compared for Chlamydia trachomatis detection in urine and in genital specimens collected with Copan flocked swabs in culture media. A protocol was also established for the highly sensitive detection of C. trachomatis in semen specimens using the cobas 4800 CT/NG test. A total of 708 consecutive urogenital samples (293 male urine samples and 356 vaginal, 45 cervical and 14 urethral swabs) obtained from the Bacteriology Department, as well as 100 consecutive semen samples collected from patients attending the Reproduction Biology Department, Bordeaux University Hospital, France, from July to September 2010, were analysed. Positive and negative agreements between the cobas 4800 CT/NG and cobas TaqMan CT tests were 92.7 % [95 % confidence interval (CI), 82.7-97.1 %] and 99.2 % (95 % CI, 98.2-99.7 %), respectively, with an overall agreement of 98.7 % (699/708). The clinical sensitivity of the cobas 4800 CT/NG assay for C. trachomatis ranged from 90.9 to 100 % depending on specimen type, with an overall prevalence of 7.2 % (51/708). The clinical specificity ranged from 99.1 to 100 % depending on specimen type. Dilution of 25 µl semen samples in cobas PCR medium proved to be the most sensitive protocol with the lowest inhibition rate. In conclusion, the cobas 4800 CT/NG test was found to be an effective method for detection of C. trachomatis in semen, male urine and genital swab samples collected dry or in universal transport medium.