Secondary Logo

Journal Logo

Original Study

Neisseria gonorrhoeae and Chlamydia trachomatis Among Women Reporting Extragenital Exposures

Trebach, Joshua D. BS*; Chaulk, C. Patrick MD*†; Page, Kathleen R. MD*†; Tuddenham, Susan MD, MPH*; Ghanem, Khalil G. MD, PhD*

Author Information
Sexually Transmitted Diseases: May 2015 - Volume 42 - Issue 5 - p 233-239
doi: 10.1097/OLQ.0000000000000248
  • Free


Recommendations from the Centers for Disease Control and Prevention only call for pharyngeal screening of Neisseria gonorrhoeae (GC) and rectal screening of GC and Chlamydia trachomatis (CT) in HIV-infected and at-risk men who have sex with men (MSM).1 There are no routine recommendations for the extragenital screening of women. The prevalence of extragenital sexually transmitted infections (STIs) in some women may be significant.2–6 Untreated pharyngeal GC, although generally asymptomatic,7 can be passed to sexual partners through oral sex.8 It has also been shown that the pharynx may be the site of resistance acquisition.9 Rectal GC and CT can present with discharge and proctitis, but are usually asymptomatic.10,11

Our aim was to examine the prevalence of extragenital GC and CT in women reporting extragenital exposures and to compare these rates with those observed in MSM and men who have sex with women (MSW) among patients accessing care at 2 public sexually transmitted disease (STD) clinics in Baltimore, MD. We determined the proportion of infections that would have been missed had only urogenital testing been performed, the number of persons needed to test to diagnose a case of extragenital CT or GC, and the predictors of extragenital infections.


This was a retrospective study from an electronic database. All patients who reported extragenital exposures in the preceding 3 months, who presented for care between June 1, 2011, and May 31, 2013, and who were tested for GC and CT using nucleic acid amplification tests (NAATs) at all sites of exposure were included in the analyses. Our clinics implemented extragenital screening for all patients who reported extragenital exposures to determine the prevalence of extragenital infections in our population and to inform the approach that the clinic would adopt for future extragenital testing. This analysis was granted approval by the institutional review board of the Johns Hopkins Medical Institutions.

Information on patients that visit either the Baltimore City Health Department Eastern Health District or the Druid Health Center is collected in an electronic patient database. Both clinical and laboratory data were recorded in this study. The clinical assessment includes a structured interview on current symptoms, STI history and behavioral risk factors, a physical examination, clinician impressions, treatment, and referrals. Patients are asked about the reason for their visit (e.g., routine checkup, contact with an infected partner, current symptoms [which included pharyngitis, urogenital discharge, dysuria, genital lesion, genital itching, rash, and irritation/odor, rectal pain, and rectal discharge]), sexual exposures (genital, oral, rectal), illicit drug use, number of sexual partners, STI history, sexual orientation, and sexual risk behaviors. Rectal exposure was defined as mouth to rectum, penis to rectum, or rectal exposure through shared sex toys. A directed physical examination on each patient includes evaluation of the oropharynx, skin, abdomen, genitals, and, when indicated, rectum. This examination documents abnormalities such as rashes, discharge, and ulcers. All findings on the history, physical examination, and outside referrals are documented on the encounter form and captured in the electronic clinical database. Laboratory data were also recorded in the database.

Extragenital gonorrhea and chlamydia were diagnosed via NAAT performed on-site at the Baltimore City Health Department laboratory using the Gen-Probe APTIMA Combo 2 Assay (Gen-Probe Inc, San Diego CA), a target amplification nucleic acid probe test that uses target capture for the in vitro qualitative detection and differentiation of ribosomal RNA from CT and GC using the TIGRIS DTS analyzer. This assay was used to detect extragenital GC and CT following in-house validation using appropriate positive and negative controls. Genital gonorrhea was diagnosed by culture and confirmed using biochemical testing (Gonocheck-II; TCS Biosciences, Buckingham, United Kingdom) in both men and women. In women, genital chlamydia was diagnosed by NAAT using a clinician-collected endocervical swab and the Gen-Probe APTIMA Combo 2 assay. Because of budgetary constraints, men were not tested for genital CT. They were diagnosed as having nongonococcal urethritis (NGU) based on Gram’s stain of urethral secretions demonstrating at least 5 white blood cells per oil immersion field and a negative urethral GC culture.1 The policy at the Baltimore City Health Department has been to screen men for NGU and to limit genital chlamydia NAATs to women. Although we do not have an accurate prevalence of genital CT in men, their extragenital CT results are provided to serve as a comparison.

We compared proportions using the χ2 test and mean values using the t test. We calculated a number needed to test to detect an isolated extragenital infection. We defined the number needed to test as 1 divided by the absolute risk reduction. Logistic regression models were used to determine predictors of extragenital infections. Variables that were assessed in the univariate models included the following: race; age; signs and symptoms (abdominal pain, genital discharge, dysuria, genital lesion, genital itching, genital odor, oral lesion, rash, rectal lesion, rectal discharge, or no symptoms); HIV status; use of oral medications for erectile dysfunction in men; use of alcohol, cocaine, heroin, or methamphetamines; needle sharing; sex for alcohol or drugs; history of intravenous (IV) drug use; sex with an HIV-infected partner; sex with MSM; history of sexual assault; and self-reported condom use during the last sexual exposure. Variables that were significant at the P = 0.20 value in the univariate regression and any biologically relevant variables were included in the multivariable models. Point estimates of odds ratios (OR) with 95% confidence intervals (CI) are presented. Two-tailed P values less than 0.05 were assumed to represent statistical significance. Data were analyzed using STATA 12.1 (STATA Corporation, College Station, TX).


There were 10,389 patients who were tested for extragenital GC and CT after reporting extragenital exposures. Their demographic, behavioral, and clinical characteristics are summarized in Table 1. Prevalence of gonorrhea and chlamydia among the different populations (women, MSW, and MSM) is also summarized in Table 1. The Venn diagram demonstrates the relationship between prevalence of extragenital and genital GC and CT infections among women (Fig. 1). Of those who reported extragenital exposures, 30.3% (95% CI, 23.4–37.9) of all cases of GC and 13.8% (95% CI, 10.7–17.6) of all cases of CT would have been missed had extragenital testing not been performed. Eighty-three women (95% CI, 63–112) would have to be tested to detect an isolated extragenital GC infection. In comparison, 8 MSM (95% CI, 6–10) and 67 MSW (95% CI, 53–88) would have to be tested to detect an isolated extragenital GC case. Similarly, 60 women (95% CI, 47–80) would have to be tested to detect an isolated extragenital CT infection. In comparison, 10 MSM (95% CI, 8–13) and 75 MSW (95% CI, 58–98) would have to be tested to detect an isolated extragenital CT case. If we were to exclude all symptomatic patients and patients who were known contacts to a confirmed case of GC and CT, 43 women (95% CI, 31–60), 6 MSM (95% CI, 5–8), and 69 MSW (95% CI, 50–99) would have to be tested to detect an isolated extragenital GC case. Similarly, 24 women (95% CI, 19–31), 10 MSM (95% CI, 7–13), and 58 MSW (95% CI, 43–82) would have to be tested to detect an isolated extragenital CT case.

Figure 1
Figure 1:
Genital and extragenitalGC (top) and CT (bottom) in women.
Demographic and Clinical Characteristics of the Study Population

In the multivariable models (Table 2), age ≤18 years was the strongest predictor of any extragenital infections in women. Age less than 18 years was significantly associated with isolated GC of the throat and CT of the rectum. No factors were significantly associated with isolated GC of the rectum and CT of the throat. Intravenous drug use was only associated with an increased risk of any pharyngeal GC. White women had a higher odds of being diagnosed as having any pharyngeal CT compared with African American women. No other variables, including clinical signs and symptoms, were significantly associated with extragenital infections in women. Age ≤ 18 years was associated with increased odds of pharyngeal GC (adjusted OR [aOR], 3.3; 95% CI, 1.6–7.0) and CT (aOR, 7.7; 95% CI, 2.9–20.3) among MSW but not MSM. When we assessed predictors of isolated extragenital infections, age <18 years was a significant predictor of throat GC and rectal CT (Table 2) but was no longer a significant predictor of GC of the rectum (aOR, 4.7; 95% CI, 0.3–77.2) and CT of the throat (aOR 1.5; 95% CI, 0.5–4.3).

Multivariable Predictors of (a) Any Extragenital Gonorrhea or Chlamydia Infection and (b) Isolated Extragenital Gonorrhea and Chlamydia Infections Among Women in Our Cohort


Most guidelines that address extragenital testing for GC and CT have focused on MSM1,12 given the burden of these infections in that population.13 Among MSM who reported extragenital sexual exposures in our clinics, the prevalence of GC and CT was 3- to 8-fold higher than that in women. The prevalence of extragenital infections in women, however, was not insignificant. The prevalence of rectal GC was higher than that of genital GC, and 30% of GC infections in women would have been missed with a genital-only testing approach. The prevalence of rectal CT was equivalent to genital CT, and approximately 15% of CT infections would have been missed if extragenital testing were not done. Our findings reflect those of other studies, summarized in Table 3, that have assessed extragenital testing in women. Most studies suggest that 20% to 40% of GC infections and 10% to 25% of CT infections in women would be missed if extragenital sites were not tested. Very few MSW reported any anal exposures, but MSW had higher rates of pharyngeal GC than do women. Their rates of pharyngeal CT were slightly lower.

A Summary of Studies That Assessed Prevalence of Extragenital Gonorrhea and Chlamydia in Women

The absolute burden of extragenital GC and CT infections is significantly different between MSM and women. This is best characterized by comparing the number of patients needed to test to diagnose a single extragenital infection: 6- to 10-fold more women would need to be tested compared with MSM to diagnose a single extragenital infection in our population. A recent study suggested that extragenital screening for GC and CT may be cost-effective among MSM in high-prevalence settings—depending on the impact of rectal CT/GC screening on HIV incidence.14 Whether extragenital screening can be cost-effective in women is not known. Extragenital infections can be transmitted to male partners,15 but trying to prevent urethritis in heterosexual men by screening for extragenital infections in their female partners may not make as compelling an argument given the lower risk of HIV acquisition among heterosexuals. Another argument is that screening for extragenital CT in women may impact chlamydia control on a population level (by preventing infections in male partners who may infect their other female partners), but the ability to measure the impact of this to inform cost-effectiveness studies is challenging. For GC, there is the theoretical risk of the throat being the site of resistance acquisition, but how that would figure into a cost-effectiveness analysis is also unclear. Indeed, the area of cost-effectiveness of extragenital testing in women represents a challenge that has yet to be fully explored.

Young age was the single most important predictor of any extragenital infections in women. Women who were younger than or equal to 18 years had nearly a 4-fold increased odds of being diagnosed as having an extragenital infection compared with older women. A similar finding was noted among MSW. Hunte et al.2 found that young age (defined as <28 years) was the only risk factor noted to be associated with extragenital infections among women attending an STD clinic in Miami. Among MSM, though, the association with young age was less pronounced: age had no impact on the detection of pharyngeal GC and CT, whereas older MSM (ages 19–30 years) had a 2-fold higher odds of being diagnosed as having rectal GC and CT. When assessing women with isolated extragenital infections, young age no longer predicted GC infection of the rectum and CT of the throat. Although both estimated ORs suggested a positive association with younger age, the confidence limits were broad either suggesting a lack of association with young age, or limited power due to a significantly reduced sample size.

This study has several limitations. Culture was used to diagnose genital gonococcal infections in both men and women. Given that culture has a lower sensitivity than NAAT, we may have overestimated the number of missed infections with a genital-only testing approach. Our estimates, however, are in line with several other sources (Table 3). Testing of extragenital sites was based on sexual history—only those who reported extragenital exposures were tested and testing occurred at the site of reported exposure. Guidelines have, in general, favored testing based on exposure history.1 Whether the prevalence of extragenital infections among women in our clinics who did not report symptoms or exposure is different from those who did is not known. Nucleic acid amplification tests are not 100% specific, so false-positive results cannot be excluded. Rectal infections may reflect cross-contamination from genital secretions. Finally, none of the NAATs are Food and Drug Administration cleared for extragenital testing. They are, however, considered the tests of choice for detecting extragenital GC and CT infections,1 and a careful in-house validation protocol was conducted to ensure optimal performance.

Although the prevalence of extragenital gonorrhea and chlamydia is highest in MSM, a significant number of gonorrhea and chlamydia cases in women would be missed with genital-only testing. Cost-effectiveness analyses are needed to help inform national guidelines on extragenital screening in young women.


1. Centers for Disease Control and Prevention. Sexually Transmitted Disease (STDs) Treatment Guidelines, 2010. Morb Mortal Wkly Rep 2010; 59: 12–13.
2. Hunte T, Alcaide M, Castro J. Rectal infections with chlamydia and gonorrhea in women attending a multiethnic sexually transmitted diseases urban clinic. Int J STD AIDS 2010; 21: 819–822.
3. Rodriguez-Hart C, Chitale R, Rigg R, et al. Sexually transmitted infection testing of adult film performers: Is disease being missed? Sex Transm Dis 2012; 39: 989–994.
4. Garner AL, Schembri G, Cullen T, et al. Should we screen heterosexuals for extra-genital chlamydial and gonococcal infections? Int J STD AIDS 2014.
5. Koedijk FDH, van Bergen JEAM, Dukers-Muijrers NHTM, et al. The value of testing multiple anatomic sites for gonorrhoea and chlamydia in sexually transmitted infection centres in the Netherlands, 2006–2010. Int J STD AIDS 2012; 23: 626–631.
6. Javanbakht M, Gorbach P, Stirland A, et al. Prevalence and correlates of rectal chlamydia and gonorrhea among female clients at sexually transmitted disease clinics. Sex Transm Dis 2012; 39: 917–922.
7. Wiesner PJ, Tronca E, Bonin P, et al. Clinical spectrum of pharyngeal gonococcal infection. N Engl J Med 1973; 288: 181–185.
8. Bernstein KT, Stephens SC, Barry PM, et al. Chlamydia trachomatis and Neisseria gonorrhoeae transmission from the oropharynx to the urethra among men who have sex with men. Clin Infect Dis 2009; 49: 1793–1797.
9. Bolan GA, Sparling F, Wasserheit JN. The emerging threat of untreatable gonococcal infection. N Engl J Med 2012; 366: 485–487.
10. Klein EJ, Fisher LS, Chow AW, et al. Anorectal gonococcal infection. Ann Intern Med 1977; 86: 340–346.
11. Quinn TC, Goodell SE, Mkrtichian E, et al. Chlamydia trachomatis proctitis. N Engl J Med 1981; 305: 195–200.
12. Carder C, Mercey D, Benn P. Chlamydia trachomatis UK testing guidelines. British Association for Sexual Health and HIV. 2010. Available at: Accessed August 12, 2014.
13. Schachter J, Moncada J, Liska S, et al. Nucleic acid amplification tests in the diagnosis of chlamydial and gonococcal infections of the oropharynx and rectum in men who have sex with men. Sex Transm Dis 2008; 35: 637–642.
14. Chesson HW, Bernstein KT, Gift TL, et al. The cost-effectiveness of screening men who have sex with men for rectal chlamydial and gonococcal infection to prevent HIV infection. Sex Transm Dis 2013; 40: 366–371.
15. Marcus JL, Kohn RP, Barry PM, et al. Chlamydia trachomatis and Neisseria gonorrhoeae transmission from the female oropharynx to the male urethra. Sex Transm Dis 2011; 38: 372–373.
16. van Liere GAFS, Hoebe CJPA, Dukers-Muijrers NHTM. Evaluation of the anatomical site distribution of chlamydia and gonorrhea in men who have sex with men and in high-risk women by routine testing: Cross-sectional study revealing missed opportunities for treatment strategies. Sex Transm Infect 2014; 90: 58–60.
17. Ladd J, Hsieh Y, Barnes M, et al. Female users of Internet-based screening for rectal STIs: Descriptive statistics and correlates of positivity. Sex Transm Infect 2014; 90: 485–490.
18. Jenkins WD, Nessa LL, Clark T. Cross-sectional study of pharyngeal and genital chlamydia and gonorrhoea infections in emergency department patients. Sex Transm Infect 2014; 90: 246–249.
19. Shaw SG, Hassan-Ibrahim M, Soni S. Are we missing pharyngeal and rectal infections in women by not testing those who report oral and anal sex? Sex Transm Infect 2013; 89: 397.
    20. Karlsson A, Osterlund A, Forssen A. Pharyngeal Chlamydia trachomatis is not uncommon any more. Scand J Infect Dis 2011; 43: 344–348.
    21. Peters RP, Nijsten N, Mutsaers J, et al. Screening of oropharynx and anorectum increases prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae infection in female STD clinic visitors. Sex Transm Dis 2011; 38: 783–787.
    22. Bachmann LH, Johnson RE, Cheng H, et al. Nucleic acid amplification tests for diagnosis of Neisseria gonorrhoeae and Chlamydia trachomatis rectal infections. J Clin Microbiol 2010; 48: 1827–1832.
    23. Tipple C, Hill SC, Smith A. Is screening for pharyngeal Chlamydia trachomatis warranted in high-risk groups? Int J STD AIDS 2010; 21: 770–771.
      24. Giannini CM, Kim HK, Mortensen J, et al. Culture of non-genital sites increases the detection of gonorrhea in women. J Pediatr Adolesc Gynecol 2010; 23: 246–252.
      25. Barry PM, Kent CK, Philip SS, et al. Results of a program to test women for rectal chlamydia and gonorrhea. Obstet Gynecol 2010; 115: 753–759.
      26. Raychaudhuri M, Birley HDL. Audit of routine rectal swabs for gonorrhoea culture in women. Int J STD AIDS 2010; 21: 143–144.
      27. Van der Helm JJ, Hoebe CJ, van Rooijen MS, et al. High performance and acceptability of self-collected rectal swabs for diagnosis of Chlamydia trachomatis and Neisseria gonorrhoeae in men who have sex with men and women. Sex Transm Dis 2009; 36: 493–497.
      28. Bachmann LH, Johnson RE, Cheng H, et al. Nucleic acid amplification tests for diagnosis of Neisseria gonorrhoeae. Oropharyngeal Infect 2009; 47: 902–907.
        29. Ostergaard L, Agner T, Krarup E, et al. PCR for detection of Chlamydia trachomatis in endocervical, urethral, rectal, and pharyngeal swab samples obtained from patients attending an STD clinic. Genitourin Med 1997; 73: 493–497.
        30. Jones RB, Rabinobitch RA, Katz BP, et al. Chlamydia trachomatis in the pharynx and rectum of heterosexual patients at risk for genital infection. Ann Intern Med 1985; 102: 757–762.
        31. Handsfield HH, Knapp JS, Diehr PK, et al. Correlation of auxotype and penicillin susceptibility of Neisseria gonorrhoeae with sexual preference and clinical manifestations of gonorrhea. Sex Transm Dis 1980; 7: 1–5.
        © Copyright 2015 American Sexually Transmitted Diseases Association