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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Med Health R I. Author manuscript; available in PMC 2013 September 5.
Published in final edited form as:
Med Health R I. 2012 August; 95(8): 252–254.
PMCID: PMC3763711

Recommendations For the Diagnosis of Neisseria gonorrhoeae and Chlamydia trachomatis, Including Extra-Genital Sites

Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the two most common reportable sexually transmitted infections (STIs) in the United States.1 Adolescent girls (15 to19 years of age) and young women (20 to 24 years of age) are at highest risk for these infections.2 This likely reflects a combination of factors, including biological differences that place females at greater risk for STIs than males, as well as higher screening rates among young women. Similarly, men who have sex with men (MSM) are at increased risk for STIs including chlamydia and gonorrhea due to higher rates of unsafe sexual behaviors. Clinicians should be aware of current screening recommendations and diagnostic methods for detection of gonorrhea and chlamydia in genital as well as extra-genital sites to address this prevailing epidemic, particularly among younger women and MSM.

Epidemiology in Rhode Island

The surveillance data on chlamydia and gonorrhea in Rhode Island are available through 2010.3 Chlamydia is by far the most commonly reported STI in Rhode Island with a total of 3,480 cases (336 per 100,000 people; 2,478 females and 1,002 males) reported in 2010; this number is unchanged over the last five years. In contrast, reported cases of gonorrhea have decreased from 508 cases in 2006 (rate of 48.0 cases per 100,000) to 291 cases in 2010 (rate of 28.1 cases per 100,000), with rates unchanged since 2008. Females comprise 42% (121/291) of gonorrhea cases, compared to 71% of chlamydia cases (2,478/3,480). However, for both infections, rates are highest in 15 to 24 year olds among both males and females. By race and ethnicity, African-Americans are most disproportionately affected followed by Hispanics and non-Hispanic whites in Rhode Island.

Clinical Presentation

Over 50% of women with chlamydia infection are asymptomatic. The most common site of infection is the urogenital tract and, when symptomatic, usually manifests as cervicitis with mucoid vaginal discharge, bleeding, and dyspareunia. Ascending infection can present with right upper quadrant pain and/or pleuritic pain consistent with perihepatitis (Fitz-Hugh Curtis syndrome). Upper genital tract infection, otherwise known as pelvic inflammatory disease (PID), can present with vaginal discharge, dysuria, lower abdominal pain, and systemic symptoms such as fever. Chlamydia-induced PID carries a higher rate of infertility for women of child bearing age than gonorrhea. In pregnant women, undiagnosed infection can cause life threatening ectopic pregnancy, premature rupture of membranes, as well as neonatal conjunctivitis and/or pneumonia.

As with their female counterparts, asymptomatic chlamydial infection is common among males, causing health care providers to frequently rely on screening tests in order to detect infection. Urogenital infection in men affecting the lower genital tract can present as a non-gonococcal urethritis or epididymitis. Symptoms include dysuria and urethral mucopurulent discharge. Identification of infection in men is of importance as they can serve as a reservoir for infection in women.

Gonorrhea infections in females most commonly involve the cervix. Females are asymptomatic approximately half of the time. Typical symptoms include a mucopurulent discharge, and the exam may demonstrate friable cervical mucosa. Other symptoms may include abdominal pain, dyspareunia, dysuria, pruritus, PID, or perihepatitis. The main impetus for the early diagnosis and treatment of gonorrhea is to prevent the development of PID. Among women, gonococcal infections might not produce recognizable symptoms until complications such as PID have occurred. PID occurs in up to 40% of women with cervical infection, and can result in tubal scarring that can lead to ectopic pregnancy or infertility.

In men, gonorrhea is asymptomatic only 10% of the time.4 The majority of urethral infections caused by N. gonorrhoeae among men produce symptoms that cause them to seek curative treatment soon enough to prevent serious sequelae, but treatment might not be soon enough to prevent transmission to others.1 Gonorrhea usually causes urethritis including dysuria and a purulent penile discharge. Furthermore, gonorrhea usually does not cause other invasive disease in men, although it may progress to cause local abscesses, prostatitis, or epididymitis.

Diagnostic Considerations

The current standard laboratory test for detection of urogenital chlamydia and gonorrhea is a nucleic acid amplification test (NAAT).5 These tests are extremely sensitive and specific for detection of both organisms (>90%) using a noninvasive urine sample, thus reducing the need for pelvic examination or urethral sampling. These tests are FDA-cleared for the diagnosis of gonorrhea and chlamydia urogenital infections. Current guidelines1,6 recommend screening all women age 25 years or younger for chlamydia and gonorrhea, as well as women older than 25 who have a history of STIs, new or multiple sex partners, or exchange sex for drugs or money. Pregnant women should be screened for all STIs. Men with risk factors for infection should be screened including gay, bisexual, transgender, or other MSM. Screening for STIs including gonorrhea and chlamydia should occur for MSM on an annual basis, and more frequently if multiple or anonymous partners or intravenous drug use is involved (as often as three to six months).

Clinicians should be aware of extra-genital mucosal sites of infection for both gonorrhea and chlamydia, specifically the oropharynx and rectum.7 Anorectal gonorrhea infection in women is usually asymptomatic. Symptoms of proctitis such as anal pruritus, discharge, and pain on defecation are seen in a minority of patients (3%).8 For women, many infections occur in the setting of urethral, vaginal, or cervical infection (46%). However, anorectal infection may be found solely in the rectum (4–6%).8,9 It is unclear whether anal infection is due to anal intercourse or due to autoinfection from a urogenital source. Gonorrheal infection of the oropharynx is also common in women, occurring in 2–6% of individuals.10,11

Among men and especially MSM, extra-genital sites of infection are common, and MSM are a high-risk group in which rates of STIs are increasing.12,13 Anorectal gonorrhea in men, compared to women, may be the only site of infection in up to 40%. Symptoms may include a purulent discharge, tenesmus, pain, and/or constipation. Infection may be due to gonorrhea alone, or may be in conjunction with other STIs including herpes simplex, chlamydia, and/or syphilis. Oropharyngeal infections are usually asymptomatic but can present with pharyngitis. Surveillance studies have suggested that the pharynx is the most common site of gonorrhea infection among MSM ranging from 3 to 15%.14,15 Interestingly, oropharyngeal gonorrhea is self-limiting with resolution of infection in the majority of cases. This may suggest that oropharyngeal treatment is unnecessary; however, the infection may be passed to the genital tract causing more invasive or disseminated disease.

Although no NAAT tests are FDA-cleared for use with rectal or oropharyngeal specimens for the diagnosis of gonorrhea and chlamydia, some laboratories have validated these specimen sites for clinical use.13 Cultures from these sites yield poor sensitivity at less than 50%. Over a 17 month period during 2011–2012, Lifespan laboratories tested a total of 32,589 and 31,201 samples for chlamydia and gonorrhea, respectively. (Table 1) Chlamydia was positive in 5.7% (111/19449) of urine specimens, (the most common specimen received for testing of CT and GC), 1.7% (5/291) of pharyngeal, and 11.8% (21/178) of rectal specimens. Gonorrhea was positive in 0.9% (159/31,201) of urine, 3.4% (11/320) of pharyngeal, and 5.3% (10/188) of rectal specimens. The high rates of oropharyngeal and rectal infections with both chlamydia and gonorrhea are consistent with previous studies demonstrating significant infection in patients selected for screening at these anatomic sites secondary to identification of risk factors.

Table 1
Anatomic site specific Chlamydia trachomatis and Neisseria gonorrhea infections as determined by nucleic acid amplification testing (NAAT).*


Aggressive STI screening of the oropharynx, rectum, and urethra should be performed in individuals who perform sexual practices involving these sites, especially in MSM. Comprehensive STI screening for chlamydia and gonorrhea should include a NAAT of the urine, rectum (for men and women who have receptive anal intercourse), and the pharynx (for men with gonorrhea and women who have receptive oral intercourse). Recognition and diagnosis of chlamydia and gonorrhea is essential to decrease the morbidity associated with these diseases, as well as prevent the transmission of other STIs including HIV.16,17


Disclosure of Financial Interests

Kimberle Chapin, MD, receives grant research support from Gen-Probe.

The authors and/or their spouses/significant others have no other financial interests to disclose.

Contributor Information

Philip A. Chan, Assistant Professor of Medicine in the Division of Infectious Diseases at the Warren Alpert Medical School of Brown University and staff physician at The Miriam and Rhode Island Hospitals.

Marjorie Janvier, Fellow in the Division of Infectious Diseases at the Warren Alpert Medical School of Brown University.

Nicole E. Alexander, Assistant Professor of Pediatrics and Medicine in the Division of Infectious Diseases at the Warren Alpert Medical School of Brown University and staff physician at The Miriam and Rhode Island Hospitals.

Erna M. Kojic, Associate Professor of Medicine in the Division of Infectious Diseases at the Warren Alpert Medical School of Brown University and staff physician at The Miriam and Rhode Island Hospitals.

Kimberle Chapin, Associate Professor of Pathology and Laboratory Medicine at the Warren Alpert Medical School of Brown University and Director of Microbiology at the Lifespan Medical Center Department of Pathology.


1. Workowski KA, Berman S. Sexually transmitted diseases treatment guidelines, 2010. MMWR Recomm Rep. 2010;59:1–110. [PubMed]
2. Sexually Transmitted Disease Surveillance. Atlanta, GA: Centers for Disease Control; 2010.
4. Sherrard J, Barlow D. Gonorrhoea in men: clinical and diagnostic aspects. Genitourin Med. 1996;72:422–6. [PMC free article] [PubMed]
5. Johnson RE, Newhall WJ, Papp JR, Knapp JS, Black CM, et al. Screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections – 2002. MMWR Recomm Rep. 2002;51:1–38. [PubMed]
6. Screening for chlamydial infection: US Preventive Services Task Force recommendation statement. Ann Intern Med. 2007;147:128–34. [PubMed]
7. Mayer KH, Bush T, Henry K, Overton ET, Hammer J, et al. Ongoing sexually transmitted disease acquisition and risk-taking behavior among US HIV-infected patients in primary care: implications for prevention interventions. Sex Transm Dis. 2012;39:1–7. [PMC free article] [PubMed]
8. Klein EJ, Fisher LS, Chow AW, Guze LB. Anorectal gonococcal infection. Ann Intern Med. 1977;86:340–6. [PubMed]
9. Stansfield VA. Diagnosis and management of anorectal gonorrhoea in women. Br J Vener Dis. 1980;56:319–21. [PMC free article] [PubMed]
10. Kraus SJ. Incidence and therapy of gonococcal pharyngitis. Sex Transm Dis. 1979;6:143–7. [PubMed]
11. Osborne NG, Grubin L. Colonization of the pharynx with Neisseria gonorrhoeae: experience in a clinic for sexually transmitted diseases. Sex Transm Dis. 1979;6:253–6. [PubMed]
12. Fox KK, del Rio C, Holmes KK, Hook EW, 3rd, et al. Gonorrhea in the HIV era: a reversal in trends among men who have sex with men. Am J Public Health. 2001;91:959–64. [PubMed]
13. Cosentino LA, Campbell T, Jett A, Macio I, Zamborsky T, Cranston RD, Hillier SL. Use of nucleic acid amplification testing for the diagnosis of anorectal sexually transmitted infections. J Clin Microb J Clin Microbiol. 2012 Jun;50(6):2005–8. [PMC free article] [PubMed]
14. Kent CK, Chaw JK, Wong W, Liska S, Gibson S, Hubbard G, Klausner JD. Prevalence of rectal, urethral, and pharyngeal chlamydia and gonorrhea detected in 2 clinical settings among men who have sex with men: San Francisco, California, 2003. Clin Infect Dis. 2005;41:67–74. [PubMed]
15. Ota KV, Fisman DN, Tamari IE, Smieja M, Ng L-K, Jones KE, et al. Incidence and treatment outcomes of pharyngeal Neisseria gonorrhoeae and Chlamydia trachomatis infections in men who have sex with men: a 13-year retrospective cohort study. Clin Infect Dis. 2009;48:1237–43. [PubMed]
16. Laga M, Manoka A, Kivuvu M, Malele B, Tuliza M, Nzila N, Goeman J. Non-ulcerative sexually transmitted diseases as risk factors for HIV-1 transmission in women: results from a cohort study. AIDS. 1993;7:95–102. [PubMed]
17. Cohen MS, Hoffman IF, Royce RA, Kazembe P, Dyer JR, et al. Reduction of concentration of HIV-1 in semen after treatment of urethritis: implications for prevention of sexual transmission of HIV-1. AIDSCAP Malawi Research Group. Lancet. 1997;349:1868–73. [PubMed]