Pooling nasopharyngeal/throat swab specimens to increase testing capacity for influenza viruses by PCR

Real-time PCR methodology can be applied to rapidly and accurately detect influenza viruses. During times of surge testing or enhanced pandemic surveillance, public health laboratories (PHLs) may experience overwhelming demand for testing, even while the prevalence of positive specimens remains low. To improve laboratory capacity and testing efficiency during surges, we evaluated whether nasopharyngeal (NP)/throat swab specimens can be pooled and tested for the presence of the 2009 H1N1 influenza virus without a reduction in sensitivity. Pools of 10 specimens were extracted and concentrated upon elution on the MagNA Pure LC instrument, and real-time PCR was performed on the Applied Biosystems 7500 Fast platform, using the CDC swine influenza virus real-time RT-PCR detection panel (rRT-PCR swine flu panel). Specimens in positive pools were singly re-extracted and retested by PCR to identify individual positive samples. Initial studies showed that spiking a pool of nine negative specimens (100 μl each) or 900 μl of virus transport medium with 100 μl of a positive clinical specimen caused no loss of sensitivity by rRT-PCR testing. Pools containing either multiple positive specimens or specimens positive for other respiratory viruses also showed no negative effect on crossing threshold (C(T)) values. To test the robustness of the pooling protocol, a panel of 50 blinded samples was sent to three PHLs and tested in five pools of 10. All PHLs correctly identified the positive specimens. This study demonstrates the feasibility of using a pooling strategy to increase capacity and conserve resources during surge testing and periods of enhanced influenza surveillance when the prevalence is low.

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.

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.

Screening for chlamydial infection

OBJECTIVES

To examine data on the effectiveness of screening for chlamydial infection by a physician or other health care professional. Specifically, we examine the evidence that early treatment of chlamydial infection improves health outcomes, as well as evidence of the effectiveness of screening strategies in nonpregnant women, pregnant women, and men, and the accuracy of tests used for screening. This review updates the literature since the last recommendation of the U.S. Preventive Services Task Force published in 1996.

SEARCH STRATEGY

We searched the topic of chlamydia in the MEDLINE, HealthSTAR, and Cochrane Library databases from January 1994 to July 2000, supplemented by reference lists of relevant articles and from experts in the field. Articles published prior to 1994 and research abstracts were cited if particularly important to the key questions or to the interpretation of included articles.

SELECTION CRITERIA

A single reader reviewed all English abstracts. Articles were selected for full review if they were about Chlamydia trachomatis genitourinary infections in nonpregnant women, pregnant women, or men and were relevant to key questions in the analytic framework. Investigators read the full-text version of the retrieved articles and applied additional eligibility criteria. For all topics, we excluded articles if they did not provide sufficient information to determine the methods for selecting subjects and for analyzing data.

DATA COLLECTION AND ANALYSIS

We systematically reviewed three types of studies about screening in nonpregnant women that relate to three key questions: (1) studies about the effectiveness of screening programs in reducing prevalence rates of infection, (2) studies about risk factors for chlamydial infection in women, and (3) studies about chlamydial screening tests in women. Our search found too few studies on pregnant women to systematically review, although pertinent studies are described. We systematically reviewed two types of studies about screening in men: (1) studies about prevalence rates and risk factors for chlamydial infection in men and (2) studies about chlamydial screening tests in men.

MAIN RESULTS

Nonpregnant women. The results of a randomized controlled trial conducted in a large health maintenance organization indicate that screening women selected by a set of risk factors reduces the incidence of pelvic inflammatory disease (PID) over a 1-year period. Changes in population prevalence rates have not been well documented because few studies have employed a representative population sample. Age continues to be the best predictor of chlamydial infection in women, with most studies evaluating cut-offs at age younger than 25 years. Other risk factors may be useful predictors, but these are likely to be population specific. To determine the accuracy of screening tests for women, we retrieved and critically reviewed 34 articles on test performance. Results indicate that endocervical swab specimens and first-void urine specimens have similar performance when using DNA amplification tests and have better sensitivity than endocervical culture. Recurrent chlamydial infections in women have been associated with increased risks for PID and ectopic pregnancies. Pregnant women. The Second Task Force recommendations for screening pregnant women were based on two major studies demonstrating improved pregnancy outcomes following treatment of chlamydial infection. We identified no recent studies on this topic in our literature search. Very few studies describe risk factors for chlamydial infection in pregnant women. Nonculture testing techniques appear to perform well in pregnant women, although studies are limited. Men. No studies described the effectiveness of screening or early treatment for men in reducing transmission to women or in preventing acute infections or complications in men. Studies of prevalence rates and risk factors for chlamydial infection in men are limited. Age lower than 25 years is the strongest known risk factor cited so far. Results of urethral swab specimens compared to first-void urine specimens were similar for DNA amplification tests. DNA amplification techniques are more sensitive than culture.

CONCLUSIONS

Screening women for Chlamydia trachomatis reduces the incidence of PID, and it is associated with reductions in prevalence of infection in uncontrolled studies. No studies were found to determine whether screening asymptomatic men would reduce transmission or prevent acute infections or complications. Age is the strongest risk factor for men and women. A variety of tests can detect chlamydial infection with acceptable sensitivity and specificity, including new DNA amplification tests that use either endocervical swabs in women, urethral swabs in men, or first-void urine specimens from men and women.

Pooling urine samples for ligase chain reaction screening for genital Chlamydia trachomatis infection in asymptomatic women

The accuracy of pooling urine samples for the detection of genital Chlamydia trachomatis infection by ligase chain reaction (LCR) was examined. A model was also developed to determine the number of samples to be pooled for optimal cost savings at various population prevalences. Estimated costs included technician time, laboratory consumables, and assay costs of testing pooled samples and retesting individual specimens from presumptive positive pools. Estimation of population prevalence based on the pooled LCR results was also applied. After individual urine specimens were processed, 568 specimens were pooled by 4 into 142 pools and another 520 specimens were pooled by 10 into 52 pools. For comparison, all 1,088 urine specimens were tested individually. The sample-to-cut-off ratio was lowered from 1.0 to 0.2 for pooled samples, after a pilot study which tested 148 samples pooled by 4 was conducted. The pooling algorithm was 100% (48 of 48) sensitive when samples were pooled by 4 and 98.4% (61 of 62) sensitive when samples were pooled by 10. Although 2.0% (2 of 99) of the negative pools of 4 and 7.1% (1 of 14) of the negative pools of 10 tested presumptive positive, all samples in these presumptive-positive pools were negative when retested individually, making the pooling algorithm 100% specific. In a population with 8% genital C. trachomatis prevalence, pooling by four would reduce costs by 39%. The model demonstrated that with a lower prevalence of 2%, pooling eight samples would reduce costs by 59%. Pooling urine samples for detection of C. trachomatis by LCR is sensitive, specific, and cost saving compared to testing individual samples.