Polymerase chain reaction (PCR) and ligase chain reaction (LCR) were compared for the diagnosis of Chlamydia trachomatis infections by testing urine specimens from 408 high school female students. After therapy, sequential urine specimens were tested to determine persistence of chlamydial DNA in urine. Baseline PCR of cervical specimens was positive in 53 (13.0%) students, and PCR and LCR of urine specimens were positive in 63 (15.4%) and 60 (14.7%), respectively. After discrepant analysis, 64 (15.7%) patients could be confirmed as truly infected. Follow-up urine specimens from 33 infected patients demonstrated that at 1 -3 days after therapy, PCR and LCR were positive for 40% and 73.3%, respectively. Only at 15 days after therapy did all specimens test negative. Urine tests for Chlamydia organisms should not be used as a test of cure within 3 weeks after treatment. Use of urine assays for screening sexually active adolescents has the potential to significantly improve control of chlamydial infections. Joint Committee for Clinical Investigation of Johns Hopkins University were women, PCR is only approved for use with urine from men followed in the conduct of this study. The study was approved by the Institu-[10]. However, research has demonstrated that PCR is highly tional Review Boards of Johns Hopkins University and the Baltimore City Health Department. sensitive (87.8%) and specific (97.6%) when urine specimens Financial support: Region III Chlamydia Program (CDC); Roche Molecular from female subjects are used [16]. Because PCR and LCR Systems (Branchburg, NJ) and Abbott Laboratories (Abbott Park, IL) donated are so exquisitely sensitive and can detect DNA from nonviable test kits.

The COBAS AMPLICOR CT/NG test for Neisseria gonorrhoeae cross-reacts with certain strains of nonpathogenic Neisseria species. In some strains, the target sequence is identical to that of N. gonorrhoeae, whereas other strains have a small number of mismatches within the regions recognized by the primers or probe used in the COBAS AMPLICOR NG test. These cross-reactive strains are occasionally present in urogenital specimens, causing false-positive results in the COBAS AMPLICOR NG test. Analysis of the data generated in a large multicenter clinical trial showed that 2.9% of the specimens gave signals between A 660 s of 0.2 and 3.5 but that one-half of these equivocal specimens did not contain N. gonorrhoeae. Most of these equivocal specimens were correctly classified as true positive or true negative by retesting in duplicate and defining a PCR-positive result as two of three results with an A 660 of >2.0. If specimens had been classified as positive or negative based on a single test result using a cutoff of an A 660 of 0.2, specificity would have ranged from 96.2 to 98.9% depending on specimen type, sex, and presence of symptoms. By employing the equivocal zoneretesting algorithm, specificity increased to 98.6 to 99.9% with little effect (0.1 to 4.9% decrease) on sensitivity in most specimen types, enabling the test to achieve a positive predictive value of at least 90% in populations with a prevalence of 4% or higher. In lower-prevalence populations, the test could be used to screen for presumptive infections that would have to be confirmed by an independent test.The COBAS AMPLICOR CT/NG test provides a powerful diagnostic tool for screening for both chlamydial and gonococcal infections. We and others have observed that the NG portion of the test (COBAS AMPLICOR NG) cross-reacts with some isolates of certain nonpathogenic Neisseria species (4). When the original, recommended cutoff (A 660 of 0.2) is used, the COBAS AMPLICOR NG test can produce false-positive results for Neisseria gonorrhoeae, presumably due to the presence of cross-reactive Neisseria species in some urogenital specimens. In one population, approximately 26% of COBAS AMPLICOR NG-positive results were false positives, which corresponded to approximately 3% of the total population (4). In contrast, the same laboratory observed fewer than 1% falsepositive results among urogenital specimens from a second population (4).In this paper, we confirm that the test does cross-react with some isolates of Neisseria subflava (4) and Neisseria cinerea and compare the target sequences in these cross-reactive species with that of N. gonorrhoeae. Using data from a multicenter trial (n ϭ 4,173 patients; prevalence ϭ 13.1%) conducted at six sites in the United States (8), we show how test sensitivity and specificity vary with the cutoff value used. We then assess whether both sensitivity and specificity can be optimized by establishing a large equivocal zone and using an algorithm that involves additional testing of specimens yielding equivocal results. Implementat...