The impact on accuracy and cost of ligase chain reaction testing by pooling urine specimens for the diagnosis of Chlamydia trachomatis infections

Detection of Chlamydia trachomatis infections by polymerase chain reaction in asymptomatic pregnant women with special reference to the utility of the pooling of urine specimens

BACKGROUND & OBJECTIVES

Genital Chlamydia trachomatis (CT) infections are one of the most prevalent sexually transmitted infections across the world. In pregnant women, if not detected and treated early, these may result in poor pregnancy outcomes and complications. The present study was aimed to screen CT infections from first void urine (FVU) samples of asymptomatic pregnant women using molecular methods. The secondary objective was to evaluate cost-effectiveness in pooling FVU samples for their diagnostic application.

METHODS

FVU samples were collected from 1000 asymptomatic pregnant women over a period of three years. Pooling was done by including five specimens in one pool in the amount of 10 μl and subjected to polymerase chain reaction (PCR) and further confirmed by direct fluorescent antibody assay (DFA).

RESULTS

The age of study participants ranged from 18 to 43 yr with the median±standard deviation of 26±3.84 yr. Majority of positive participants were younger than 25 years. A total of 200 pools were prepared and 20 of these were PCR positive. When individual specimen in 20 positive pools was tested, 20 PCR-positive specimens were identified from 19 pools, of which 16 were positive by DFA. Thus, CT was detected in 1.6 per cent asymptomatic pregnant women in India and pooling strategy resulted in 70 per cent reduction in a number of tests performed.

INTERPRETATION & CONCLUSIONS

Our study detected C. trachomatis infection in 1.6 per cent asymptomatic pregnant women, and pooling of FVU specimens for PCR testing was found to be a cost-saving strategy in comparison to testing individual samples. Further evaluation and studies on the bigger sample size are warranted to validate these results.

New point of care Chlamydia Rapid Test--bridging the gap between diagnosis and treatment: performance evaluation study

OBJECTIVE

To evaluate the performance of a new Chlamydia Rapid Test with vaginal swab specimens as a potential tool for chlamydia diagnosis and screening.

DESIGN

Performance evaluation study. Settings A young people's sexual health centre (site 1) and two genitourinary medicine clinics (sites 2 and 3) in the United Kingdom.

PARTICIPANTS

1349 women aged between 16 and 54 attending one of the three clinics.

MAIN OUTCOME MEASURES

Sensitivity, specificity, positive predictive value, and negative predictive value of the Chlamydia Rapid Test versus polymerase chain reaction and strand displacement amplification assays; correlation between the Chlamydia Rapid Test visual signal and organism load; acceptability to participants of self collected vaginal swabs as the specimen type for Chlamydia testing.

RESULTS

Polymerase chain reaction positivity rates for Chlamydia trachomatis infection were 8.4% (56/663) at site 1, 9.4% (36/385) at site 2, and 6.0% (18/301) at site 3. Compared with polymerase chain reaction assay, the resolved sensitivity, specificity, positive predictive value, and negative predictive value of the Chlamydia Rapid Test were 83.5% (91/109), 98.9% (1224/1238), 86.7% (91/105), and 98.6% (1224/1242). Compared with strand displacement amplification assay, sensitivity and specificity of the Chlamydia Rapid Test were 81.6% (40/49) and 98.3% (578/588). Organism load of self collected vaginal swabs ranged from 5.97x10(2) to 1.09x10(9) Chlamydia plasmids per swab, which correlated well with the Chlamydia Rapid Test's visual signal (r=0.6435, P<0.0001). Most (95.9%) surveyed participants felt comfortable about collecting their own swabs.

CONCLUSIONS

The performance of the Chlamydia Rapid Test with self collected vaginal swabs indicates that it would be an effective same day diagnostic and screening tool for Chlamydia infection in women. The availability of Chlamydia Rapid Test results within 30 minutes allows for immediate treatment and contact tracing, potentially reducing the risks of persistent infection and onward transmission. It could also provide a simple and reliable alternative to nucleic acid amplification tests in chlamydia screening programmes.

Pooling of urine specimens allows accurate and cost-effective genetic detection of Chlamydia trachomatis in Lithuania and other low-resource countries

The aims of this study were to compare performance characteristics and cost-effectiveness of pooling urine samples for screening and diagnosis of Chlamydia trachomatis using Digene Hybrid Capture II CT/NG Test (HCII), and to examine the prevalence of C. trachomatis in male military recruits in Lithuania. A total of 410 urine samples were individually tested and pooled by 5 and 10 samples, respectively. The sensitivity and specificity of diagnosis were not affected by either pooling strategy. The estimated population prevalence of C. trachomatis infection was nearly identical, i.e. 4.4%, 4.4% and 4.1% based on individually tested samples, and samples pooled by 5 and 10, respectively. For this estimation of the population prevalence, pooling 5 samples reduced the costs by 80% and pooling 10 samples reduced the costs by 90%. For diagnosis of each individual sample, the pooling strategies resulted in cost savings of 60% (5 samples per pool) and 56% (10 samples per pool). The present pooling strategies were sensitive, specific and cost-efficient for screening and diagnosis of C. trachomatis infection in male military recruits in Lithuania. The strategies would be most useful for reasonably inexpensive large-scale screening, prevalence studies and even diagnostics in Lithuania and many other low-resource countries.

Sexually transmitted Chlamydia trachomatis, Neisseria gonorrhoeae, and HIV-1 infections in two at-risk populations in Barcelona: female street prostitutes and STI clinic attendees

OBJECTIVE

To determine the prevalence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and HIV-1 infections in female street prostitutes and STI clinic attendees in Barcelona.

DESIGN

This was a prospective study carried out in two four-month periods over two years. Urine specimens were tested for CT and NG using a PCR pooling algorithm. Among street prostitutes HIV-1 testing in urine was also carried out.

RESULTS

The prevalences of CT, NG, and HIV-1 in female street prostitutes (n=301) were 4.7%, 3.7%, and 1.0%, respectively. Women from Eastern Europe had the highest prevalence of CT (p=0.01). Prevalences of CT, NG, and HIV-1 among all clinic attendees (n=536) were 4.3%, 4.5%, and 4.4%, respectively. Prevalence of HIV-1 infection among homosexual men was higher compared with heterosexual men and women (p<0.001).

CONCLUSIONS

Overall CT prevalence is currently lower than in other European countries, although it could increase as a result of immigration. Rates of HIV-1 and of NG are higher among homosexual than among heterosexual men.

Nucleic acid amplification testing for Neisseria gonorrhoeae: an ongoing challenge

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

Use of pooled urine samples and automated DNA isolation to achieve improved sensitivity and cost-effectiveness of large-scale testing for Chlamydia trachomatis in pregnant women

The success of large-scale screening for Chlamydia trachomatis depends on the availability of noninvasive samples, low costs, and high-quality testing. To evaluate C. trachomatis testing with pregnant women, first-void urine specimens from 750 consecutive asymptomatic pregnant women from the Rotterdam area (The Netherlands) were collected. Initially, we investigated the performance of three different DNA isolation methods with 350 of these urines and 70 pools of 5 of the same subset of urine samples. The routinely used COBAS AMPLICOR test was compared to the COBAS AMPLICOR test with prior DNA isolation by use of the MagNA Pure large-volume kit and the MagNA Pure bacterial DNA isolation kit. The latter combination provided the best DNA test for pooled urines, with a sensitivity twice that of the other methods. Next, using all 750 urines, the COBAS AMPLICOR performance for individual testing was compared to pooled testing with the standard COBAS AMPLICOR procedure and subsequently to pooled testing with COBAS AMPLICOR in combination with the MagNA Pure bacterial DNA isolation kit. The sensitivity of COBAS AMPLICOR was 65% on individual and 42% on pooled urines but improved to 92% on pooled urines with the MagNA Pure bacterial DNA isolation kit, making this combination the best screening method. The C. trachomatis prevalence in this population appeared to be 6.4%. Additionally, the cost of the combined MagNA Pure bacterial DNA isolation kit and COBAS AMPLICOR method on pooled urines was only 56% of the cost of the standard COBAS AMPLICOR test applied to individual urines. Costs per positive case detected in the combined method were 39% of standard costs.

Utility of pooled urine specimens for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in men attending public sexually transmitted infection clinics in Mumbai, India, by PCR

Pooling urogenital specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by nucleic acid amplification tests is an attractive alternative to individual testing. As pooling can reduce the costs of testing as well as labor, it has been advocated for use in resource-poor settings. However, it has neither been widely adopted nor evaluated for use in developing countries. We evaluated the practical use of pooling first-catch urine (FCU) specimens for the detection of C. trachomatis and N. gonorrhoeae from 690 men in Mumbai, India, by PCR. FCU, urethral smears, and swabs were collected from men seen at two sexually transmitted infection (STI) clinics. All laboratory testing was done at the Lokmanya Tilak General Hospital. Gram stain smears and culture isolation for N. gonorrhoeae were performed. Each FCU was tested individually and in pools using the Roche Amplicor PCR for C. trachomatis and N. gonorrhoeae with an internal control for inhibition. Specimen pools consisted of aliquots from five consecutively processed FCUs combined into an amplification tube. An optical density reading of > or =0.20 indicated a pool for which subsequent testing of individual samples was required. Prevalence by PCR on single specimens was 2.2% (15/690) for C. trachomatis and 5.4% (37/690) for N. gonorrhoeae. Compared to individual FCU results, pooling for C. trachomatis and N. gonorrhoeae had an overall sensitivity of 96.1% (50/52). Specificity was 96.5% (83/86) in that three pools required single testing that failed to identify a positive specimen. Pooling missed two positive specimens, decreased the inhibition rate, and saved 50.3% of reagent costs. In this resource-limited setting, the use of pooling to detect C. trachomatis and N. gonorrhoeae by PCR proved to be a simple, accurate, and cost-effective procedure compared to individual testing.

Pooling of clinical specimens prior to testing for Chlamydia trachomatis by PCR is accurate and cost saving

The accuracy and cost savings of pooling specimens prior to testing for Chlamydia trachomatis by PCR were evaluated with genital and urine specimens (n = 2,600). There was a 60% reduction in tests without significant loss of accuracy. The efficiency of pooling vaginal swabs is demonstrated for the first time.

Cost-effectiveness of universal screening for chlamydia and gonorrhea in US jails

Universal screening for the sexually transmitted diseases (STDs) of chlamydia and gonorrhea on intake in jails has been proposed as the most effective strategy to decrease morbidity in inmates and to reduce transmission risk in communities after release. Most inmates come from a population that is at elevated risk for STDs and has limited access to health care. However, limited resources and competing priorities force decision makers to consider the cost of screening programs in comparison to other needs. The costs and cost-effectiveness of universal screening in correctional settings have not been documented. We estimated the incremental cost-effectiveness of universal urine-based screening for chlamydia and gonorrhea among inmates on intake in US jails compared to the commonly used practice of presumptive treatment of symptomatic inmates without laboratory testing. Decision analysis models were developed to estimate the cost-effectiveness of screening alternatives and were applied to hypothetical cohorts of male and female inmates. For women, universal screening for chlamydia only was cost-saving to the health care system, averting more health care costs than were incurred in screening and treatment. However, for men universal chlamydia screening cost $4,856 more per case treated than presumptive treatment. Universal screening for both chlamydia and gonorrhea infection cost the health care system $3,690 more per case of pelvic inflammatory disease averted for women and $650 more per case of infection treated for men compared to universal screening for chlamydia only. Jails with a high prevalence of chlamydia and gonorrhea represent an operationally feasible and cost-effective setting to universally test and treat women at high risk for STDs and with limited access to care elsewhere.

Comparison of the Becton Dickinson strand displacement amplification and Cobas Amplicor Roche PCR for the detection of Chlamydia trachomatis: pooling versus individual tests

The objective of the study was to examine the influence of pooling Chlamydia trachomatis specimens. We compared Becton Dickinson ProbeTec strand displacement amplification (SDA) with Cobas Amplicor Roche (PCR). With PCR as the standard, SDA performed equally well in single-sample testing. For pooled PCR samples (compared to individual PCR), we found a sensitivity of 100% and a specificity of 98.9%. For pooled SDA tests (compared to individual SDA), we found a sensitivity of 86.5% and a specificity of 98.9%. Our conclusion is that 2-sucrose phosphate buffer (2-SP) can be used for individual SDA testing. A reduced sensitivity was found for pooled SDA samples, and we cannot recommend that SDA be used for pooling with 2-SP. Further pooling studies with other transport media are warranted.

Developments in the screening for Chlamydia trachomatis: a review

Many studies have evaluated selective screening criteria for women in various settings. Most have concluded and all guidelines recommend that all women aged < 25 be screened yearly for C. trachomatis infection. Behavioral criteria, such as the number of sex partners, new or more than one sex partners, and previous infection, also can serve as criteria for screening women aged > 25. Because re-infection rates are high and occur within a few months, complications may be reduced further if partners are treated and women rescreened 4 to 6 months after initial infection. Revised recommendations for C. trachomatis screening programs have stated that more frequent screening may be considered among women < 20 and those with recent infection. Screening in nontraditional settings and careful evaluation of local prevalence and risk factor information should be encouraged. Private providers and emergency room providers should discuss screening recommendations and adopt a C. trachomatis screening policy for the population they serve. The HEDIS measure should serve to encourage at least annual screening of 15- to 25-year-old sexually active females through providers linked to managed care organizations. In general, high yields (ie, percentage of tests that are positive) in nontraditional settings and enhanced feasibility and acceptability of urine-based tests may encourage further innovative approaches to reach and screen populations at risk. Several issues remain to be addressed to increase the effectiveness of screening efforts. If more sensitive amplification tests are used widely, more infected persons will be identified and treated, and transmission patterns may change, particularly if partner treatment also occurs. Current screening criteria should continue to be re-evaluated. An important issue that affects testing methods includes the possible need for confirmation testing when using NAATs if the prevalence of C. trachomatis is less than 2%. If the sensitivity of an NAAT is 85% and specificity is 99%, in a hypothetical population of 10,000 with a prevalence of 2%, the positive predictive value is 170/268 (63%). A second important issue affecting testing methods and feasibility of using NAATs for screening large numbers of individuals is the pooling of urine specimens, which has been evaluated in several studies and found to be very effective for reducing costs. A research issue for pooling is the determination of the most cost-effective prevalence levels for pooling. An additional research question is in which populations should a NAAT be used for detection of C. trachomatis and N. gonorrhoeae. There are no recommendations for the routine screening of men because of the paucity of data showing that this strategy can reduce sequelae. The CDC is conducting a multisite study to examine the feasibility, acceptability, and usefulness of screening of asymptomatic men. There are a few studies have determining cost-effective prevalence threshold levels, particularly with NAATs. A recently developed decision analysis model by CDC designed to maximize the effectiveness of screening strategies for C. trachomatis infections may be useful for decision makers. It is intended to serve as an easy and flexible tool to determine cost effectiveness at a local level and takes into account positivity rates and test performance characteristics (SOCRATES). It is unclear if recurrent infection is caused by true re-infection by the same or a different partner or recurrence of initial infection. Recurrence may be caused by persistence of C. trachomatis or antibiotic resistance. This distinction is of scientific interest because the appropriate intervention differs (eg, identification of risk factors for the former and microbiologic investigations for the latter). Effective partner management and retesting are critical to reducing sequelae of C. trachomatis infection. Screening for C. trachomatis infection remains an essential component of C. trachomatis control. It is cost effective, most infections are asymptomatic, and symptom-based health care seeking and testing identify few of those infected. The likelihood that opportunities for screening are missed is high particularly in non-STD clinic settings. Local studies using NAATs to determine C. trachomatis prevalence and risk factors are helpful to health care providers so they can make evidence-based decisions on who to screen. The use of nontraditional, non-clinic-based test settings should be explored further. We have focused on summarizing the medical evidence regarding recommendations for screening for C. trachomatis. High-risk populations for C. trachomatis infection may overlap with populations for other STDs, and comprehensive STD prevention programs that involve a range of STD service providers are needed to successfully reduce the STD-related health burden in the population.

Prevalence of Chlamydia trachomatis infections and specimen collection preference among women, using self-collected vaginal swabs in community settings

BACKGROUND

Chlamydia trachomatis is a common, often asymptomatic sexually transmitted infection.

GOAL

The goal was to estimate the prevalence and predictors of C. trachomatis among young women using self-collected vaginal swabs, and the preferences of women and physicians for self-testing.

STUDY DESIGN

A total of 514 attendees of university/college health clinics, adolescent birth control clinics, centers providing health services to homeless youth and adults (street health centers), a sexually transmitted diseases clinic, and family practices were tested by ligase chain reaction. Preference for self- versus provider-testing was examined.

RESULTS

Prevalence was 6.0% and was highest (18.2%) in the street health centers. In multivariate analysis, only recent contact with someone with C. trachomatis infection was significantly associated with infection (odds ratio, 7.1; 95% confidence interval, 2.5-20.0). Most women (54.2%; 256 of 472) preferred self-sampling compared with physician sampling (15.9%; 75 of 472). The majority of physicians (75.0%; 9 of 12) reported at the start and end of the study that they would use vaginal swab self-sampling if available.

CONCLUSIONS

Prevalence of infection in young women attending homeless youth organizations was high. Self-sampling was acceptable and could facilitate screening in high-risk women who do not regularly access health services.

Multisite pooling study using ligase chain reaction in screening for genital Chlamydia trachomatis infections

BACKGROUND

Ligase chain reaction (LCR), a nucleic acid amplification assay, is a highly specific and sensitive test for detecting Chlamydia trachomatis in cervical and urethral swabs as well as first-void urine specimens.

GOAL

To examine the suitability of using the LCR test to detect C trachomatis in pooled cervical specimens.

STUDY DESIGN

The performance of LCR in pooled specimens was compared with individual specimen testing at six laboratories using 3,170 cervical swab specimens randomly selected from specimens received for routine testing in the participating laboratories. These samples then were combined consecutively into 634 pools of 5 specimens and 317 pools of 10 specimens. A reduced sample to cutoff ratio of 0.2 or more was used for the pooled specimens.

RESULTS

Of the 188 positive specimens (98.9%), 186 were identified when single specimens were analyzed. When pools of 5 or 10 specimens were evaluated, 99.5% and 98.9% of the positive swabs, respectively, were identified correctly. Two positive specimens were detected only through pooling.

CONCLUSIONS

Pooling samples for detection of C trachomatis by LCR is sensitive and specific. Depending on the prevalence of infection (positivity), LCR testing may result in cost savings, as compared with individual testing of specimens.

Pooling of Chlamydia laboratory tests to determine the prevalence of ocular Chlamydia trachomatis infection

With the Global Elimination of Trachoma by 2020 program underway, it has become increasingly important to identify the prevalence of ocular chlamydia infection in communities. DNA amplification tests are the gold standard, but are prohibitively expensive. In the present paper, we investigate whether pooling multiple specimens into a single test is feasible. The conjunctivae of 170 children in western Nepal were examined and swabbed. The prevalence of chlamydial infection was estimated in two ways using the ligase chain reaction: by testing all 170 specimens individually, and by testing 34 pools of 5 specimens each. We show that the confidence interval for 34 pooled specimens approaches that of doing all 170 specimens as the prevalence decreases. We also determine the optimal number of specimens to pool into a single test to minimize the confidence interval of the estimate. If the population prevalence is expected to be around 10%, then 14 specimens should be pooled per test. Even at 50% prevalence, costs can be reduced by pooling two samples per test.

Chlamydia, gonorrhea, and HIV-1 prevalence among five populations of women in the Czech and Slovak Republics

BACKGROUND

Five populations at risk for sexually transmitted diseases (STDs) in the Czech and Slovak Republics were sampled.

GOAL

To estimate prevalence of Chlamydia trachomatis, Neisseria gonorrhoeae, and HIV-1 infections.

STUDY DESIGN

Urine specimens were collected serially from women at a Prague prenatal clinic (n = 134), a Prague dermatovenerealogy clinic (n = 91), sex workers from northern and central Bohemia (n = 35), students from a northern Bohemian school (n = 217), and Gypsies from Jarovnice, Slovakia (n = 128). These specimens were tested for chlamydia and gonorrhea using a ligase chain reaction pooling algorithm, and for HIV using an enzyme immunoassay confirmed by Western blot.

RESULTS

The prevalence of chlamydia was 2.2% (95% CI, 0.4-6.4) in the prenatal clinic, 5.5% (95% CI, 1.8-12.4) in the STD clinic, 22.9% (95% CI, 10.4-40.1) among street sex workers, 8.2% (95% CI, 3.6-15.6) among sexually active female high school students, and 3.9% (95% CI, 1.3-8.9) among Gypsy women. Gonorrhea was found in only two populations: 2.2% (95% CI, 0.3-7.7) in the STD clinic, and 2.9% (95% CI, 0.1-14.9) among sex workers. No HIV-1 infection was detected.

CONCLUSIONS

Urine screening was an efficient and accurate method for identifying groups at risk for STDs in the Czech Republic and Slovakia because sample collection was fast and noninvasive, and potential participation bias was reduced by high acceptability.

Diagnosis and treatment of common sexually transmitted diseases in women

Chlamydia trachomatis and Neisseria gonorrhoeae are 2 very common sexually transmitted organisms, whose clinical manifestations in women can range from an asymptomatic carrier state to active pelvic inflammatory disease with known serious sequelae, including chronic pelvic pain, infertility, and ectopic pregnancy. The economic and clinical burden of these 2 infectious organisms are significant in the sexually active population. New developments in diagnosis and treatment of these infections raise great hope that substantial reduction in morbidity and disease prevalence rates can be achieved. Herpes simplex virus is probably better publicized and more feared in the sexually active population, and is far more prevalent than previously recognized; fortunately, however, it is not generally associated with significant morbidity. This article will review the current diagnoses and treatments of these conditions and consider some of the issues surrounding the impact of screening asymptomatic sexually active individuals. The treatment guidelines will emphasize the 1998 Guidelines for Treatment of Sexually Transmitted Diseases from the Centers for Disease Control and Prevention.

New tests for bacterial sexually transmitted diseases

Recent advances in diagnostic tests for sexually transmitted diseases include the development of a synthetic Venereal Disease Research Laboratory reagent that will improve the sensitivity and stability of nontreponemal serologic tests for syphilis. A second generation user friendly and high throughput nucleic acid amplification test for Chlamydia trachomatis and Neisseria gonorrhoeae has also been developed.

Pooling cervical swabs and testing by ligase chain reaction are accurate and cost-saving strategies for diagnosis of Chlamydia trachomatis

Specimen pooling to achieve efficiency when testing urine specimens for Chlamydia trachomatis nucleic acids has been suggested. We pooled endocervical swabs from 1,288 women and also tested individual swabs by ligase chain reaction (LCR). Out of 53 positive specimens, pools of 4 or 8 specimens missed two positives, providing 96.2% accuracy compared to individual test results. Dilution and positive-control spiking experiments showed that negative specimens with inhibitors of LCR in the pool reduced the signal. Conversely, two extra positives, detected only through pooling, were negative by individual testing but became positive after storage, suggesting that fresh positive specimens with labile inhibitors may be positive in a pool because of dilution of inhibitors. For this population of women with a 4% prevalence of C. trachomatis infection, substantial savings in cost of reagents (55 to 63%) and technologist time (50 to 63%) made pooling strategies a desirable alternative to individual testing.