Use of NAATs to Detect Chlamydia in Children Being Evaluated for Suspected Sexual Abuse

By Margaret R. Hammerschlag, MD

The 2006 Centers for Disease Control and Prevention (CDC) STD Treatment Guidelines recommended that NAATs can be used to detect C. trachomatis in children being evaluated for suspected sexual abuse if culture is not available and if positive results can be confirmed1. Confirmation was specified as use of another NAAT that utilized a different genetic target. The 2010 STD Guidelines now recommend that NAATs can be used in children with some limitations.

There were 3 published studies that compared NAATs to C. trachomatis culture in children being evaluated for suspected sexual abuse published before 20092-4. All were from the US. Two studies evaluated LCR and an additional study evaluated PCR. Two of the studies primarily evaluated girls, most of whom were postpubertal and many were consensually sexually active. These studies utilized LCR, an assay which was removed from the mar-ket in 20025. One of these studies evaluated PCR in addition to LCR. There were major limitations, including failure to use an independent reference standard in estimating test performance, and failure to separately analyze test performance by age and gender (when applicable). The third study evaluated PCR and an EIA to culture and also included many postpubertal girls. The data from these studies were insufficient to make any recommendation on the use of NAATs in children being evaluated for suspected sexual abuse.

In order to generate data on the performance of NAATs in prepubertal children, CDC sponsored a multicenter study which was published in 20096. The study evaluated the use of SDA and TMA using urine and genital swabs (vagina and urethra) compared to culture for diagnosis of C. trachomatis in 536 children (485 girls and 51 boys), 0-13 years of age being evaluated for sus-pected sexual abuse/assault at four tertiary care centers in the United States (Houston, TX, Atlanta, GA, Harrisburg, PA and Brooklyn, NY). Cultures for C. trachomatis were performed at the clinical or hospital laboratories of each center, according to their own standard protocols. All sites transported swab specimens at
4°C for C. trachomatis culture in either commercial Chlamydial or viral transport medium. Culture protocols at all sites included the isolation of C. trachomatis in cyclo-heximide-pretreated McCoy cells, either in shell vials, 24-well, or 96-well tissue culture plates. The commercial NAAT tests were performed at the CDC (SDA and TMA). All samples were processed and tested according to manufacturers’ protocols except for the TMA tests which were performed on previously frozen urine or swabs collected in the BD ProbeTec sample collection medium. Test results that were positive by SDA for C. trachomatis were confirmed using an in-house PCR targeting the ompA gene, performed at the CDC. None of the 51 boys were positive for C. trachomatis. Fifteen (3.1%) of 485 girls had a positive result for C. trachomatis by any test (7 [1.4%] by culture; 11 [2.3%] by vaginal NAAT; 13 [2.7%] by urine NAAT). None of the male participants had any positive cultures or NAATs for C. trachomatis. All participants who had a positive vaginal culture for C. trachomatis also had positive urine NAAT. Two prepubertal female children had positive C. trachomatis cultures from rectal swab specimens, but negative vaginal swab specimens by both culture and NAATs, and negative urine NAATs. No other participants had positive rectal cultures. There were no discrepant results in any of the participants tested by two commercial NAATs for C. trachomatis (ProbeTec and Aptima 2). All C. trachomatis-positive results were confirmed to be true positives by DNA sequence genotyping. Only one girl had a discrepant result for C. trachomatis (vaginal swab negative, urine positive). The sensitivity of vaginal culture for C. trachomatis was 39% in all girls studied. In contrast, the sensitivities of urine and vaginal swab NAATs were 100% and 85% in all female children, respectively, for detection of C. trachomatis. Urine may be the preferred specimen in prepubertal girls.

The results of this study suggest that NAATs, specifically SDA and TMA, can be used for detection of C. trachomatis in girls being evaluated for suspected sexual abuse. However, some limitations apply: 1. As the prevalence of C. trachomatis in this population is low, confirmatory testing is necessary 2. One cannot extrapolate from these results to other NAATs, specifically PCR. 3. One cannot extrapolate to extragential specimens. 4. One cannot make any recommendations on the use of these assays in any site in prepubertal boys. Performing a confirmatory NAAT may be problematic as most hospital laboratories only use one assay. Some of the more recently available commercial NAATs, such as TMA (Aptima 2), offer an alternate target confirmation method that can be used on the same testing platform, however there are no data on the use of this confirmatory test in this setting. Additional options include sending blinded specimens to an independent or reference laboratory for confirmation testing, confirming a NAAT-positive result by culture test (requires a separate, invasive specimen), or use of a second, alternate technology commercial NAAT.

The 2010 CDC Guidelines state that “NAATs can be used for detection of C. trachomatis in vaginal specimens or urine from girls. All specimens should be retained for additional testing if necessary. No data are available regarding the use of NAATs in boys or for extragential specimens (e.g. those obtained from the rectum) in boys and girls. Culture remains the preferred method for extragential sites.”. However the CDC cannot recommend a specific test or manufacturer. All NAATs are not equivalent. As new NAATs become available they will have to be evaluated for this indication. In addition we also need more studies on the performance of these assays in boys and for extragential sites in children. Acquiring these data are very important as identification of C. trachomatis in a prepubertal child has significant legal as well as medical implications.


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