Neisseria gonorrhoeae is a nonmotile, non-spore-forming, Gram-negative coccus that characteristically grows in pairs (diplococci), with flattened adjacent sides in the configuration of "coffee beans." All Neisseria species, including Neisseria meningitidis, rapidly oxidize dimethyl- or tetramethyl-paraphenylene diamine, the basis of the diagnostic oxidase test. The cell envelope of N. gonorrhoeae is similar to that of other Gram-negative bacteria. Specific surface components of the envelope have been related to adherence, tissue and cellular penetration, cytotoxicity, and evasion of host defenses, both systemically and at the mucosal level.

Stratified squamous epithelium can resist invasion by the gonococcus, whereas columnar epithelium is susceptible to it. Gonorrhea can occur in the genitalia of males or females without signs or symptoms. The primary infection can also occur in the rectal or pharyngeal mucosa of either sex. Gonococci attach to the mucosal epithelium and then penetrate between and through the epithelial cells to reach the subepithelial connective tissue by the third or fourth day of infection. An inflammatory exudate quickly forms beneath the epithelium. In the acute phase of infection, numerous leukocytes accumulate (many with phagocytosed gonococci), causing a characteristic profuse yellow-white discharge in males. In the absence of specific treatment, the inflammatory exudate in the subepithelial connective tissue is replaced by macrophages and lymphocytes. Direct extension of the infection occurs through the lymphatic vessels and less often through the blood vessels. Acute urethritis is the most common manifestation in males, and the infection can then spread to the posterior urethra, Cowper's glands, seminal vesicles, prostate, and epididymis, which leads to perineal, perianal, ischiorectal, or periprostatic abscesses.

Conjunctivitis beyond the newborn period follows direct spread of the gonococcus, usually via fingers contaminated with genital secretions. It rarely results from gonococcemia. Conjunctivitis is often severe, with profuse purulent discharge, chemosis, eyelid edema, and ulcerative keratitis, and presentations may mimic orbital cellulitides.

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