Molecular Detection ofChlamydia trachomatisandNeisseria gonorrhoeae

A nucleic acid amplification test (NAAT) may enable the laboratory to detect Chlamydia trachomatis and Neisseria gonorrhoeae with high sensitivity and specificity in traditional urogenital swabs and in different types of samples obtained noninvasively by patients at home or in other settings. This chapter provides guidance in selecting the most appropriate NAATs for C. trachomatis and N. gonorrhoeae among available commercial and in-house assays. The selection of targets for detection of C. trachomatis and N. gonorrhoeae is a major point in determining which assay to use for routine diagnostics. Sequence variation in the target region may lead to false-negative results, whereas the presence of the target gene in other species may lead to false-positive results. Routine diagnostics of C. trachomatis infections is predominantly performed with commercial NAAT high-volume test systems, but there are still applications where in-house-developed methods are useful. The number of samples in a pool depends on the prevalence, and it is calculated from the number of samples, which needs to be tested individually from positive pools. Samples from a negative pool should be reported as negative. The rapid spread of a mutant variant of C. trachomatis in Sweden escaping detection by some NAATs has been a warning that vigilance for drug-resistant mutants should be enforced.