Specimens submitted in M5 medium for cell culture detection of Chlamydia trachomatis were tested by nucleic acid amplification testing (NAAT) and in cell cultures. Of 35 (genital) and 26 (nongenital) specimens positive for C. trachomatis, 21 and 14 specimens, respectively, were detected exclusively by NAAT. NAAT is significantly (P < 0.0001) more sensitive than cell culture and should be considered the new "gold standard" for the laboratory diagnosis of C. trachomatis infections.Chlamydia trachomatis is the most common cause of reportable cases of sexually transmitted infections (7, 16). Sensitive, Food and Drug Administration (FDA)-approved nucleic acid amplification testing (NAAT) has replaced poorly standardized cell culture methods for the laboratory diagnosis of these infections (5,13,15,17).Specimens submitted to our laboratory with a specific request for C. trachomatis culture in M5 medium (Remel, Lenexa, KS) were inoculated into cell cultures and simultaneously processed by NAAT for both C. trachomatis and Neisseria gonorrhoeae (BDProbeTec ET). The goal of our study was to assess the performance characteristics of NAAT as a possible exclusive replacement for cell cultures for the testing of all specimens submitted for the laboratory diagnosis of C. trachomatis infections.Shell vials containing cycloheximide-treated McCoy cells (Diagnostic Hybrids Inc., Athens, OH) on coverslips were inoculated with 0.1 ml of the specimen extract in M5 transport medium and centrifuged at 700 ϫ g for 60 min. Cell cultures were incubated at 35°C for 48 h, stained with fluoresceinconjugated monoclonal antibody specific for C. trachomatis (Trinity Biotech Co., Wicklow, Ireland), and examined at 200 ϫ for the detection of C. trachomatis-infected cells (18).For NAAT, specimens (200 l) in M5 medium were placed into BD diluent, lysed by heating at 114°C for 30 min, and assayed by the BDProbeTec ET system using the BD Viper (BD Biosciences, Sparks, MD) for sample processing and detection of C. trachomatis and N. gonorrhoeae following the manufacturer's instructions.Of 383 genital specimens (cervix, 179; vagina, 166; urethra, 38) submitted to Mayo Clinic for cell culture diagnosis of C. trachomatis infections processed also by NAAT, 14 (3.7%) were positive for the organism by both methods (Table 1). Two specimens (cervix) were toxic in cell culture, and diagnostic results were not available by that method. In addition, 21 specimens were exclusively positive for C. trachomatis by NAAT (150% increase in the rate of detection compared with that of cell cultures). These 21 discrepant results were confirmed as positive by direct fluorescent antibody to specifically detect the elementary bodies of C. trachomatis (Tables 1 and 2). Importantly, there were no specimens that were detected by culture that were not detected by NAAT (100% specificity) ( Table 1). Of the 35 (14 plus 21) NAAT-positive C. trachomatis specimens, 5 (cervix, 4; vagina, 1) (14.3%) were also positive for both C. trachomatis and N. gonorrhoeae (Table 2). In addition,...