**12. Molecular methods**

**Probe tests:** There are commercially available hybridization-based tests to detect *Chlamydia trachomatis* directly from clinical specimens. In these tests, a singlestranded DNA probe labeled with a chemiluminescent substance that is complementary to the ribosomal 16sRNA of the target organism can be used. The sensitivity and specificity of this test are good [11].

**Nucleic acid amplification test:** These tests use molecular methods such as polymerase chain reaction (PCR), chain removal, and transcription-based amplification. NAATs have very high specificity like culture, but differently, it is not dependent on the viability of the causative microorganism and so sample transfer is easier. Today, the results have been accelerated by the use of fluorescent labeled probes and automatic nucleic acid extraction. The use of two target gene regions in NAATs enabled the detection of new variants. Bead-based extraction systems further increased the specificity and sensitivity of the test. Therefore, NAATs have become the gold standard in the diagnosis of *C. trachomatis* infections [10]. For these tests, first urine, vagina, cervix, and urethra swab samples are suitable. Approval studies are ongoing for non-genital (conjunctiva, oropharynx, and rectum) specimens [11]. There are also multiplex real-time PCR tests where other sexually transmitted infectious agents (*Mycoplasma genitalium*, *Tricomonas vaginalis*, *Neisseria Gonorrhoeae* vb.) can be detected [24].

*The Laboratory Diagnosis of* Chlamydia *Infections DOI: http://dx.doi.org/10.5772/intechopen.110464*

**Drekt fluorescent antibody (DFA) tests:** These tests are used in newborns, conjunctival samples. They are stained with labeled monoclonal antibodies developed against species-specific antigens on chlamydia major outer membrane protein (MOMP). Stained preparations are examined by fluorescence microscopy and samples containing fluorescent smooth-sided round or oval elementary bodies are considered positive [26].

**Enzyme immunoassay (EIA):** The enzyme immunoassay detects genus-specific antigens in elementary bodies and is less sensitive than NAAT and is not widely used [26].

**Culture:** Compared to NAATs, culture is a difficult, costly, delayed, and less sensitive method. Swabs from the endocervix, anal canal, urethra, and conjunctiva are suitable specimens for culture. Swab samples are inoculated into McCoy, HeLa229, and Buffalo Green Monkey Kidney cell lines [10]. Samples are incubated at 35–37°C and 48–72 hours. A second inoculation is performed to increase sensitivity. Intracytoplasmic inclusions are examined by direct immunofluorescence [11].

**Serology:** An increase in serum antibody titers is observed in acute genital chlamydia infections. Antibodies are raised against the infecting immunotype. Serum antibodies are higher titer than trachoma. In societies with a high prevalence of genital chlamydia infection, there is a high background of antichlamydial antibodies. Therefore, serology is not useful and common in diagnosis [26].

**Treatment:** In chlamydia infections, simultaneous treatment of sexual partners to prevent reinfection is the basic principle. Tetracyclines (such as doxycycline) are widely used in nongonococcal urethritis and in non-pregnant infected women. Azithromycin is effective and can be used in infected pregnant women. Topical treatment is not helpful in eye infections due to chlamydia so systemic treatment is preferred. Treatment with doxycycline and erythromycin for 2–3 weeks is recommended [16].
