Updated Guidelines for the Management of Gonorrhea and Chlamydia in Patients With HIV

Elizabeth A. Asiago-Reddy, MD, MSc


July 18, 2018

The Sexually Transmitted Infections (STIs) Guideline Committee of the New York State Department of Health AIDS Institute recently released updated guidelines addressing best practices for the screening, diagnosis, treatment, and management of gonorrhea and chlamydia in patients with HIV. Although focused on the management of STIs in people with HIV, this clear and comprehensive set of recommendations is relevant to many patients regardless of HIV status. The guidelines are particularly helpful because they promote optimal STI screening and management in persons who are at higher risk, including men who have sex with men (MSM) and transgender individuals. Given the growing burden of gonorrhea and chlamydia nationwide,[1] optimizing screening and treatment are the keys to reducing the risk for complications associated with these infections, such as chronic pelvic pain, infertility in women, and disseminated infections.

Sexual History and STI Screening

It is critical for HIV and primary care providers to include STI screening and sexual history in regular clinical practice. The state of New York recently adopted a policy that allows registered nurses to conduct such screening under non–patient-specific orders, which can help streamline these practices.[2] An open-minded, nonjudgmental approach to regular inquiry about sexual activity is likely to enhance a clinician's ability to diagnose and treat STIs. The guidelines provide links to online and in-person training on taking a patient's sexual history and recommendations for screening methods that accommodate varied sexual practices, including use of "the five Ps" to elicit sexual history:

  1. Partners: How many? Are they men, women, or both?

  2. Practices: How frequently, and what type (ie, vaginal, anal, or oral)? Anatomy may be varied for transgender individuals.

  3. Prevention of pregnancy: Which method(s)?

  4. Protection from STIs: How often and with whom are condoms used?

  5. Past history of STIs: Diagnoses and dates.

Even in an accommodating environment, some patients will not feel comfortable discussing details of their sexual practices with their healthcare providers. For this reason, opt-out approaches that incorporate routine screening are ideal.[3] Toward that end, the guidelines recommend at least annual screening for gonorrhea and chlamydia (and syphilis) for all patients with HIV unless a patient specifically opts out. Screening every 3 months is recommended for higher-risk patients, including those who have had a recent bacterial STI, have multiple or anonymous partners, engage in transactional sex or sex parties, or use recreational substances during sex.

The Where and How of STI Testing

The guidelines also review the "where" and "how" of STI testing. Nucleic acid amplification tests (NAATs) are strongly preferred over culture for screening because of their greater sensitivity in detecting gonorrhea and chlamydia.[4] In women, vaginal swabs are more sensitive than urine samples.[5]

Also strongly recommended is testing of all body sites that have been involved in sexual activity rather than focusing only on genital sites. Three-site testing (genital, pharyngeal, and rectal) is particularly important for MSM and transgender women (those who were assigned male sex at birth but who identify as women), and should be performed routinely.[6] Testing only reported sites of contact has been shown to be unreliable, and the prevalence of extragenital infections in these groups is so high that more than half of STIs are likely to be missed with genital screening alone.[6]

Not all laboratories have protocols for extragenital NAATs. The guidelines reference approved laboratories in New York state and include recommendations for laboratories interested in validating the testing of such specimens.

Finally, evidence indicates that self-swabbing of pharyngeal, vaginal, and rectal sites yields accurate diagnoses and is an alternative to provider-conducted swabs,[7,8] although self-swabbing should not entirely replace physical examination.

Presentation and Diagnosis

The presentation of these STIs in patients with or without HIV is typically asymptomatic, especially in women and those with extragenital infections. Urethritis in men classically presents with urethral discharge or dysuria. Women may have pelvic pain, dyspareunia, vaginal discharge or spotting, or dysuria. Rectal infections may present with rectal pain, discharge, bleeding, or anal itching. Pharyngeal gonorrhea should be considered in the differential diagnosis of a sore throat, although pharyngeal chlamydia is thought to be largely asymptomatic.

Patients with severe rectal symptoms or inguinal lymphadenopathy who test positive for chlamydia may have lymphogranuloma venereum (LGV), which is caused by the L1, L2, and L3 serovars of Chlamydia trachomatis; LGV is different from the typical infections caused by serovars D-K. Specialized antibody or polymerase chain reaction tests for LGV may provide a definitive diagnosis, but LGV is typically diagnosed on the basis of clinical examination.


The NYSDOH AIDS Institute guidelines for the treatment of patients with HIV who have gonorrhea or chlamydia mirror the recommendations of the Centers for Disease Control and Prevention for all patients.[9] Of greatest importance, gonorrhea at any site should be treated with two antibacterial agents from different classes to avoid treatment failure and the development of drug resistance. Although resistance to third-generation cephalosporins remains low in the United States, a cluster of cases in Hawaii may portend a worrisome increase.[10] Resistance to quinolones has become widespread, and resistance to oral cephalosporins and azithromycin is growing.[11]

The preferred regimen for pharyngeal, genital, or rectal gonorrhea is a single dose of ceftriaxone 250 mg by intramuscular injection plus azithromycin 1 g by mouth. Patients with mild or moderate penicillin allergy can be safely treated with this regimen. Those who require an alternative regimen should receive a single dose of gentamicin 240 mg by intramuscular injection plus azithromycin 2 g by mouth. Only when no other options are available should a patient receive an oral-only treatment regimen of a single dose of cefixime 400 mg plus azithromycin 1 g.[12] Oral-only regimens should not be used to treat pharyngeal gonorrhea because of the risk for treatment failure and promotion of drug resistance.

The preferred treatment for uncomplicated chlamydia at genital, pharyngeal, or rectal sites is a single dose of azithromycin 1 g by mouth, or doxycycline 100 mg by mouth twice daily for 7 days as an alternative. The guidelines recommend treatment of pharyngeal chlamydia with standard regimens to reduce the risk for transmission of this typically asymptomatic infection. Patients with known or suspected LGV should be treated with doxycycline 100 mg by mouth twice daily for 21 days.


Patients who are asymptomatic after completing treatment for gonorrhea or chlamydia should be retested for infection after 3 months. Patients with persistent symptoms after treatment for gonorrhea may be retested with culture after 3-5 days of treatment, but NAAT should be delayed until at least 7 days after treatment. NAAT results for chlamydia can remain positive for up to 3 weeks after treatment. The differential diagnosis in patients with persistent symptoms includes reinfection; incomplete elimination of the original infection; drug resistance; or an alternative diagnosis, such as Mycoplasma genitalium, Trichomonas vaginalis, or herpes simplex virus infection.


Reporting of gonorrhea and chlamydia is mandated by most states and has been automatically incorporated into many laboratory systems. Instructions for reporting to local health departments are included in the guidelines for those who do not have access to automated laboratory reporting. If a patient is diagnosed with gonorrhea or chlamydia, all of that patient's sex partners from the past 60 days should be empirically treated with the standard regimen for the specific infection. The risk for HIV exposure in uninfected partners of people with HIV should be evaluated as appropriate, keeping in mind that patients who maintain an undetectable viral load do not transmit HIV to their partners.

In New York, expedited partner therapy is an option. Clinicians can offer prescriptions for expedited partner therapy for patients diagnosed with chlamydia to deliver to their sex partners from the past 60 days. Partner services can assist in anonymous notification of contacts reported by patients with reportable STIs. Ideally, MSM and transgender women identified as partners of patients with any STI should undergo full screening and evaluation, given their higher overall risk for concurrent STIs.

Regularly testing for gonorrhea and chlamydia using NAATs at sites of sexual contact, promptly treating infected patients with recommended regimens, and reaching out to partners for treatment whenever possible are the keys to stemming the spread of these infections and promoting healthy sex.


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