Nucleic Acid Amplification Testing Detects Extragenital STIs Missed by Cultures in Young HIV-Infected Patients

Emma Hitt, PhD

March 12, 2010

March 11, 2010 (Atlanta, Georgia) — Nucleic acid amplification testing (NAAT) for gonorrhea and chlamydia at extragenital sites might detect more positive cases than does the use of cultures at these sites, according to a new study.

Natalie Neu, MD, from the Department of Pediatrics at Columbia University in New York City, and colleagues presented the findings here at the 2010 National STD Prevention Conference.

The researchers conducted a prospective study in 33 patients, aged 18 to 24 years, infected with HIV. Overall, 29 patients were male (24 gay or bisexual) and 4 were female. They used NAAT to test for Neisseria gonorrhoeae and Chlamydia trachomatis at 3 body sites: urethral, rectal, and pharyngeal. They compared NAAT results with those of cultures of rectal and pharyngeal sites. All positive tests were confirmed with secondary amplification assays.

Of the 434 tests conducted, 34 (7.8%) were positive — 18 for chlamydia (13 rectal, 2 pharyngeal, and 3 urethral) and 16 for gonorrhea (8 rectal, 5 pharyngeal, and 3 urethral).

Overall, only 4 of 25 patients (16%) with rectal or pharyngeal infections with gonorrhea or chlamydia had a urethral infection with gonorrhea or chlamydia at the same time, highlighting the importance of testing at extragenital sites, the Columbia team emphasized.

In addition, in no case was a positive urethral NAAT associated with the presence of a rectal or pharyngeal chlamydia infection (0 of 2 and 0 of 13, respectively). Only 2 of 4 patients with positive pharyngeal NAAT for gonorrhea and 2 of 6 patients with positive rectal NAATs also had a positive urethral NAAT.

The authors note that 74% of these infections "would have gone untreated had only a urethral NAAT been done."

The study also demonstrated that cultures were less effective than NAATs. Only 5 of 28 patients who tested positive with NAAT also tested positive with a culture. Conversely, all positive cultures also had positive NAATs, underscoring the superiority of NAAT over cultures in this setting.

"The culture has been, until recently, the gold standard for identifying gonorrhea and chlamydia in rectal and pharyngeal sites," said study author John Nelson, PhD, CPNP, from the New York Presbyterian Hospital in New York City. "However, these findings suggest that NAAT improves detection of rectal and pharyngeal [C trachomatis] and [N gonorrhoeae], compared with culture," he told Medscape Infectious Diseases at the poster session.

According to Dr. Nelson, some studies have indicated a volume of HIV up to 100 times greater in the semen of a man or in the vaginal fluids of a woman with a urethral sexually transmitted infection (STI). "So having an STI makes the transmission of HIV to an uninfected partner much more likely to happen."

However, the US Food and Drug Administration has not approved NAAT use for rectal and pharyngeal sites. According to Dr. Nelson, many clinics in areas of high HIV incidence are using NAAT testing over cultures to identify extragenital STIs, but "it varies at each location as to when NAAT testing is done — whether the person, male or female, is symptomatic or whether they just report having unprotected anal intercourse or oral receptive intercourse," he said.

"NAAT is considered the most accurate diagnostic test available for chlamydia and gonorrhea," said Julius Schachter, PhD, from the University of California, San Francisco, and director of the Chlamydia Laboratory at San Francisco General Hospital. "NAAT has been evaluated in men who have sex with men, but the fact that this study was conducted in an HIV-positive young population of both males and females is new," he told Medscape Infectious Diseases.

According to Dr. Schachter, the incidence of chlamydia and gonorrhea infections in extragenital sites is high, and if NAAT is not used, 50% of these infections can be missed.

"NAATs are approved for cervical and urethral swabs, urines, and vaginal swabs collected in clinics, but not for pharynx and rectum, and unfortunately, use for those indications will not be cleared in the near future," he said.

The study was not commercially funded. Dr. Nelson and Dr. Schachter have disclosed no relevant financial relationships.

2010 National STD Prevention Conference (NSTDP): Abstract P79. Presented March 9, 2010.

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