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

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.

Optimal specimen collection and transport methods for the detection of avian influenza virus and Newcastle disease virus

Background

Active and passive surveillance for avian influenza virus (AIV) and Newcastle disease virus (NDV) is widespread in commercial poultry worldwide, therefore optimization of sample collection and transport would be valuable to achieve the best sensitivity and specificity possible, and to develop the most accurate and efficient testing programs. A H7N2 low pathogenicity (LP) AIV strain was selected and used as an indicator virus because it is present in lower concentrations in swabbings and thus requires greater sensitivity for detection compared to highly pathogenic (HP) AIV. For similar reasons a mesogenic strain of NDV was selected. Using oro-pharyngeal and cloacal swabs collected from chickens experimentally exposed to the viruses we evaluated the effects of numerous aspects of sample collection and transport: 1) swab construction material (flocked nylon, non-flocked Dacron, or urethane foam), 2) transport media (brain heart infusion broth [BHI] or phosphate buffered saline [PBS]), 3) media volume (2 ml or 3.5 ml), 4) transporting the swab wet in the vial or removing the swab prior to transport, or transporting the swab dry with no media, and 5) single swabs versus pooling 5 or 11 swabs per vial.

Results

Using real-time RT-PCR (rRT-PCR), virus isolation (VI) and commercial antigen detection immunoassays for AIV we observed statistically significant differences and consistent trends with some elements of sample collection and transport; media, dry transport and swab construction. Conversely, the number of swabs pooled (1, 5 or 11) and whether the swab was removed prior to transport did not impact virus detection. Similarly, with NDV detection by both VI and rRT-PCR was not affected by the numbers of swabs collected in a single vial (1, 5 or 11).

Conclusions

We observed that flocked and foam swabs were superior to non-flocked swabs, BHI media was better than PBS, and transporting swabs wet was better for virus recovery and detection than transporting them dry. There was no observable difference in detection whether the swab was removed prior to transport or left in the vial. Also, with both AIV and NDV, there was no observed difference in virus detection between pools of 1, 5 or 11 swabs.

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.

Nucleic acid amplification tests for gonorrhea and chlamydia: practice and applications

Nucleic acid amplification tests (NAATs), which are highly sensitive and specific, have provided the ability to use alternative sam-ple types for the diagnosis of sexually transmitted infections (STIs). Self-collected genital specimens, such as urine or even vaginal swabs, can now be accurately used to diagnose gonorrhea or chlamydia infections. In many cases, use of these sample types can decrease the necessity for a clinician to perform a pelvic examination on women or to collect a urethral swab from men, thus extending the diagnostic capability for detecting these infections to nonclinic screening venues. As most chlamydia infections and many gonorrhea infections are asymptomatic, the use of NAATs for self-collected samples greatly increases the types and numbers of patients that can be screened outside of clinic settings. Self-sampling also allows clinicians to easily screen patients in the clinic for STIs who are not presenting for pelvic or urogenital examinations. The application of NAATs to self-collected specimens has the potential to augment public health programs designed to control the epidemic of STIs in the community.

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.

Urine nucleic acid amplification tests for the diagnosis of sexually transmitted infections in clinical practice

PURPOSE OF REVIEW

With the advent of highly sensitive and specific nucleic acid amplification assays, this report will demonstrate that self-collected genital specimens, such as urine or even vaginal swabs can be accurately used to diagnose sexually transmitted infections.

RECENT FINDINGS

Use of self collected samples can eliminate the necessity of a clinician to perform a pelvic examination for women or collect a urethral swab for men, thus extending the diagnostic capability for sexually transmitted infections to non-clinic screening venues. As many sexually transmitted infections are asymptomatic, this ability to use self-sampling greatly increases the numbers of patients that can be screened, and has the potential to augment public health programs designed to control the epidemic of sexually transmitted infections in the community. Patient collected samples are highly acceptable, highly accurate, and are becoming widely used. Self-sampling also allows clinicians to easily screen patients in the clinic, who are not presenting for pelvic or urogenital examinations, for sexually transmitted infections.

SUMMARY

Highly accurate molecular tests and easily obtained self-collected urogenital samples represent the ideal combination for obtaining the public health goal of decreasing the sexually transmitted infection epidemic among sexually active persons in the United States today.

The laboratory diagnosis of Chlamydia trachomatis infections

Lower genital tract infections with Chlamydia trachomatis are predominantly asymptomatic in men and women. Diagnostic technology has provided several approaches to the diagnosis of C trachomatis. Outside of cells, Chlamydia can die or degrade without optimal storage and transportation. Because some of the other assays perform better on certain specimen types, it is important for laboratories to recognize these differences and provide advice to physicians and nurses collecting patient specimens, with the objective of diagnosing lower genital tract infections to prevent transmission and upper tract damage. Most invasive specimens, such as cervical or urethral swabs, may be collected for culture, antigen or nucleic acid detection. Noninvasive samples such as first-void urine and vaginal swabs can be easily collected by the patient; these samples must be tested by more sensitive nucleic acid amplification tests. These newer investigative strategies should enable implementation of screening programs to identify and treat partners. Serology has not been particularly useful for the diagnosis of acute C trachomatis infections in adults. Presently, it appears that antibiotic-resistant C trachomatis is not a clinical problem. Laboratories providing C trachomatis diagnosis require participation in continuous quality improvement programs.

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.

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.

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.

Chlamydia trachomatis diagnostics

Nucleic acid amplification (NAA) assays for the diagnosis of Chlamydia trachomatis infections started to appear in the peer reviewed literature about 12 years ago and during that period we have seen an incredible effort put into the development and evaluation of commercially developed NAA kits to diagnose and treat infections.

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

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

Effect of endocervical specimen adequacy on ligase chain reaction detection of Chlamydia trachomatis

Several studies have demonstrated that the sensitivity of a commercially available PCR test for the detection of Chlamydia trachomatis (Roche Diagnostics) is affected by the cellular quality of the endocervical swab specimens. The cellular adequacies of 1,633 female endocervical swab specimens were assessed and compared with the results of C. trachomatis detection obtained by ligase chain reaction (LCR; Abbott Laboratories). Specimen adequacy studies and LCR were performed with samples from the same swab, after demonstration of the stability of human epithelial cells in LCR transport medium. Prior to heat treatment of the swab specimen, an aliquot was removed and cytocentrifuged onto a slide. Cell spots were stained and examined at x 400 magnification for endocervical (columnar epithelial or metaplastic) cells and erythrocytes. The overall rate of positivity of the LCR was 6.5% (106 of 1,633 specimens) with pooled specimens (pools of 4 specimens each; reduced cutoff). Of the 1,633 specimens examined, 655 (40.1%) were found to contain one or more endocervical cells. The rate of positivity for C. trachomatis was 10.8% (71 of 655 specimens) among specimens containing endocervical cells, whereas it was 3.6% (35 of 978 specimens) among specimens lacking endocervical cells (P < 0.0001). There was no linear trend between the rate of positivity for C. trachomatis and the number of endocervical cells (P = 0.24). The rate of positivity for C. trachomatis was 5.4% (8 of 147 specimens) among specimens containing large numbers of erythrocytes (> or =100 per high-power field), whereas it was 6.6% (98 of 1,486 specimens) among specimens containing less than 100 erythrocytes per high-power field (P = 0.59). These results show that the sensitivity of the Abbott C. trachomatis LCR test is affected by the presence of endocervical cells. Additionally, they indicate that the presence of a single endocervical cell is as good an indicator of specimen adequacy as the presence of many endocervical cells. The presence of a large number of erythrocytes was not associated with an increased rate of sensitivity of the LCR.

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.

Strategies for signal amplification in nucleic acid detection

Many aspects of molecular genetics necessitate the detection of nucleic acid sequences. Current approaches involving target amplification (in situ PCR, Primed in situ Labeling, Self-Sustained Sequence Replication, Strand Displacement Amplification), probe amplification (Ligase Chain Reaction, Padlock Probes, Rolling Circle Amplification) and signal amplification (Tyramide Signal Amplification, Branched DNA Amplification) are summarized in the present review, together with their advantages and limitations.

Evaluation of laboratory testing methods for Chlamydia trachomatis infection in the era of nucleic acid amplification

Diagnostic tests presently available for Chlamydia trachomatis have widely varying performance characteristics. To assess evolving laboratory testing practices since the introduction of nucleic acid amplification tests (NAAT), we surveyed laboratories in Washington State about their testing practices in 1998 and compared our findings to a similar survey conducted in 1995. Laboratory directors of 61 (87%) of 70 laboratories performing chlamydial tests in 1998 returned a survey. Between 1995 and 1998, 36 laboratories discontinued chlamydial testing, and the total number of laboratories performing tests in the state decreased from 92 to 70, a 24% decline. Of the 36 laboratories that discontinued testing, 25 (69%) had previously used rapid tests. While no laboratory routinely used NAAT in 1995, ligase chain reaction (LCR) was used in 23% of laboratories in 1998 and accounted for 113,624 (36%) of the 318,133 tests performed that year. Among the remaining 204,509 tests performed in 1998, other tests employed included DNA probe (29%), enzyme immunoassay (20%), culture (12%), direct fluorescent antibody assays (3%), and rapid tests (<1%). The majority (65%) of tests performed in 1998 using technologies other than LCR or culture were done in laboratories that did more than 10,000 tests. Cost and loss of revenue to laboratories were the most frequently cited reasons for not adopting NAAT. We conclude that in Washington State, NAAT have been rapidly adopted in larger laboratories, but most patients are still tested with much less sensitive technologies. Financial constraints represent the major barrier to more widespread use of DNA amplification tests.

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.