The keys to management of chlamydial infections are (1) arriving at the correct diagnosis and (2) ensuring that the patient complies with treatment.
Undiagnosed chlamydia can progress to pelvic inflammatory disease (PID), which may lead to relative or absolute infertility. This may be tragic if it occurs early in life before childbearing. Diagnostically evaluate all cases of suspected sexual abuse using chlamydial culture, not nonculture techniques.
Because of the personal nature and time-intensive diagnosis of sexually transmitted diseases (STDs), many physicians err by presuming that symptoms of an STI are caused by a urinary tract infection (UTI); therefore, patients often present with a history of multiple UTIs when, in fact, they may have had 1 or more STDs.
Adolescents are at high risk for noncompliance with treatment, especially if a patient is attempting to keep information away from parents. Single-dose, in-office treatment is increasingly being used to improve compliance and confidentiality. Partner treatment is crucial for prevention of reinfection.
Many clinicians err on the side of caution and hospitalize patients whenever PID is a concern or compliance with therapy is problematic. Consider PID an absolute indication for admission because of the potential for infertility and the poor compliance of many adolescents with prolonged treatment regimens.
Begin antibiotic therapy as soon as possible. Consider compliance, cost, and potential adverse effects. Consider treatment for possible gonorrhea coinfection. Send specimens from sites of infection to the lab for culture. Perform a pregnancy test; this can alter antibiotic treatment and patient follow-up care.
Consult obstetrics/gynecology for any patient with severe PID and any pregnant patient with chlamydial infection. Consult ophthalmology for patients with chlamydial conjunctivitis. Provide information and counseling to prevent future STDs, and consider referral for HIV testing. Encourage the patient to abstain from sexual intercourse until after treatment and testing of all partners is completed.
Two broad anatomical treatment categories of genital C trachomatis infection are recognized, as follows:
C trachomatis cervicitis/urethritis/epididymitis (D-K biovars): Lower genital tract or uncomplicated
C trachomatis salpingitis/endometritis (D-K biovars): Upper genital tract or complicated
Treatment of genitourinary chlamydial infection is clearly indicated when the infection is diagnosed or suspected. Chlamydiae are susceptible to antibiotics that interfere with DNA and protein synthesis, including tetracyclines, macrolides, and quinolones.  CDC recommends azithromycin and doxycycline as first-line drugs for the treatment of chlamydial infection. [33, 40] Medical treatment with these agents is 95% effective. Alternative agents include erythromycin, levofloxacin, and ofloxacin.  Rifalazil, a rifamycin that is highly active against C trachomatis and has a long half-life, has shown promise as a single-dose treatment for chlamydial nongonococcal urethritis and is currently being evaluated in women with uncomplicated genital infection. 
For many years, standard therapy for uncomplicated genital tract infection has been doxycycline 100 mg orally twice daily for 7 days. However, azithromycin given as a single 1-g dose is as effective as a 7-day course of doxycycline. [49, 50] The FDA released a warning on March 12, 2013, that azithromycin can cause potentially life-threatening arrhythmias. Patients with known QT-interval abnormalities or who take drugs to treat arrhythmias should receive doxycycline instead. Test of cure after treatment is unnecessary, but retesting is recommended at 3 months after therapy because of the high risk of reinfection in women and men. 
Azithromycin has also been shown to be effective in the treatment of nongonococcal urethritis, whether related to C trachomatis, genital mycoplasmas, or other organisms.  Ofloxacin 300 mg twice daily for 7 days and levofloxacin 500 mg once daily for 7 days are included as alternative agents in the 2015 CDC treatment guidelines  Azithromycin is now available as a generic drug, and its cost in the authors’ STD clinic (Indianapolis, IN) of about 60 cents per 1-g does is comparable to a 7-day course of doxycycline. A once-daily preparation of doxycycline (WC2031) was shown to be noninferior to the standard twice-daily regimen in both men and women and has been FDA approved for treatment of uncomplicated chlamydial genital infection in men and women. 
Lower genital infections caused by Chlamydia can be treated with single-dose, directly observed treatment. This practice is encouraged when possible to reduce noncompliance due to cost, confidentiality issues, motivational issues, and maturity issues.
Upper genital tract disease must be vigorously sought out because potential complications are serious, especially in adolescents. With the advent of newer, more sensitive DNA and antigen detection kits that use urine specimens instead of a pelvic examination, the potential to presume a chlamydial infection in uncomplicated lower tract disease is concerning.
Inadequately treated PID can lead to sepsis, infertility, and chronic pelvic pain. Many practitioners strongly advise admission for inpatient therapy and monitoring of response whenever PID is suspected because of a tendency of adolescents to minimize or ignore symptoms and eschew follow-up.
The management of PID, even when gonorrhea is present, should always include therapy directed against C trachomatis, as well as N gonorrhoeae and anaerobic bacteria. Randomized trials have shown that parenteral and oral regimens have similar clinical efficacy for mild to moderate PID, although doxycycline is given orally if possible because intravenous infusion is painful