Because of the medical-legal implications, the identification of a sexually transmitted disease, especially Chlamydia trachomatis and Neisseria gonorrhoeae, in a prepubertal child requires the use of methods with the highest specificity. Diagnosis of C trachomatis infection in this setting has been based on isolation of the organism in tissue culture. Culture requires careful specimen collection and stringent transport conditions with maintenance of the cold chain and requires 48–72 hours to perform. In addition, culture methods for C trachomatis are not standardised and there can be significant variation in performance from laboratory to laboratory.¹ Obtaining appropriate specimens requires a vaginal swab in children. Similarly, the definitive diagnosis of gonorrhoea has been based on culture of N gonorrhoeae, which entails isolation on selective media. Although culture of N gonorrhoeae is relatively inexpensive and highly sensitive, it is logistically complicated. As with the collection of specimens for culture of chlamydia, detection of N gonorrhoeae also requires vaginal swabs in children. The invasive nature of the specimens needed creates additional trauma for victims of sexual assault.

The introduction of nucleic acid amplification tests (NAAs) has been the most important advance in the field of chlamydia diagnostics since tissue culture replaced inoculation of eggs for culture and isolation of C trachomatis from clinical specimens. Because nucleic acid amplification is exquisitely sensitive, theoretically capable of detecting as little as a single gene copy, and highly specific, it offers the opportunity to use non-invasive sampling—that is, urine. There are now four NAAs approved by the US Food and Drug Administration (FDA) for the detection of C trachomatis in clinical specimens: polymerase chain reaction (PCR), Amplicor Chlamydia trachomatis test (Roche Molecular Diagnostics), ligase chain reaction (LCR), LCx Chlamydia trachomatis Assay (Abbott Diagnostics), transcription mediated amplification (TMA) (GenProbe), and strand displacement amplification (SDA) (ProbeTec, Becton Dickson). PCR, LCR, …