Due to the asymptomatic nature of pharyngeal gonococcal infection, testing persons at risk for pharyngeal gonococcal infection is optional, although most providers routinely test MSM. Culture is the only approved test. Pharyngeal cultures are positive in 15% to 54% of children with genital gonococcal infections (12). Because organisms are found in the base of tonsillar crypts, it is recommended to obtain Gram stain and culture specimens from deep within the crypts. Pharyngeal infection almost always coexists with genital infection, and genital cultures should also be obtained. A typical Gram stain reveals intracellular Gram-negative diplococci. This finding should be confirmed on culture on modified Thayer-Martin medium because the pharynx can be colonized by other Neisseria species. Acute HIV infection should also be considered in the differential diagnosis of pharyngitis in persons with appropriate risk factors.

The Gram stain for diagnosis of gonorrhea is considered to be positive if typical Gram-negative diplococci are seen in association with polymorphonuclear leucocytes. A positive Gram stain from a male urethral specimen is highly sensitive and specific for gonococcal infection; however, in females, the adult cervix and the vagina of prepubertal children may be colonized with other Neisseria species, rendering the Gram stain less reliable. Similarly, Gram-stained smears of rectal and pharyngeal specimens are not useful to determine infection at these sites.

Diagnostic specimens of the pharynx, rectum, and vagina or urethra should be taken and immediately plated onto selective media appropriate for isolation of N. gonorrhoeae (e.g., Thayer-Martin media) and then placed in an atmosphere enriched with carbon dioxide, which is done most easily using an extinction candle jar. Isolation of gonococci from sites containing many saprophytic organisms (vagina, cervix, pharynx, and rectum) is enhanced if selective media containing antibiotics (e.g., Thayer-Martin media) are used; these media inhibit most of the normal flora and permit only the growth of gonococci and meningococci. Specimens from other usually sterile sites (blood, synovial fluid, or cerebrospinal fluid) should be inoculated only onto nonselective (antibiotic free) media such as enriched chocolate agar. N. gonorrhoeae organisms are Gram-negative, oxidase-positive diplococci, and their presence should be confirmed with additional tests, including rapid carbohydrate tests, enzyme-substrate tests, and rapid serologic tests. Failure to perform appropriate confirmatory tests may lead to misidentification of other organisms as N. gonorrhoeae.

Although culture of N. gonorrhoeae is well standardized and widely available, there have always been concerns about the loss of viability during transport to the laboratory. Enzyme immunoassays for detection of N. gonorrhoeae were introduced in the 1980s but were not satisfactory in terms of sensitivity or specificity. In the late 1980s, a nonamplified DNA probe was introduced (PACE 2, GenProbe, San Diego, California, U.S.A.). The overall sensitivity of the DNA probe compared with that of culture of endocervical specimens from women has been on the order of 95%. Data are similar for male urethral specimens, with sensitivities of 98.8% to 100% and specificities >99% compared with culture. There are now four nucleic acid amplification tests (NAATs) approved by the U.S. Food and Drug Administration (FDA) for the detection of N. gonorrhoeae in clinical specimens: PCR (Amplicor, Roche Molecular Diagnostics, Pleasanton, California, U.S.A.); transcription-mediated amplification (TMA) (GenProbe, San Diego, California, U.S.A.); and strand displacement amplification (SDA) (ProbeTec, Becton Dickson, Franklin Lakes, New Jersey, U.S.A.). PCR and SDA are DNA amplification tests; TMA is an RNA amplification assay. A fourth NAAT, ligase chain reaction (LCX assay, Abbott Diagnostics, Abbott Park, Illinois, U.S.A.) was withdrawn from the market by the manufacturer in 2002 because of poor quality control.

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