Diagnostic Methods

Clinical reference laboratories can provide diagnostic testing for Chlamydia pneumoniae infections using culture, serology, or molecular methods (see chart below). Currently, there are multiple commercially available systems for the detection of C. pneumoniae infection, including several Food and Drug Administration (FDA)-cleared tests. Real-time Polymerase Chain Reaction (PCR) is the preferred method of diagnostic testing for acute C. pneumoniae infection, assuming the availability of an appropriate specimen type. When additional or specialized testing is necessary, local or state public health laboratories can provide either diagnostic support or forward specimens to CDC.

Advantages, Disadvantages, and Availability of Select C. pneumoniae Diagnostic Methods

Advantages, Disadvantages, and Availability of Select C. pneumoniae Diagnostic Methods
Method Advantages Disadvantages Test Setting Recommendations 7
  • Recovered isolates are ideal for genotyping and antimicrobial susceptibilities testing
  • Variety of acceptable specimen types 1
  • Time-consuming (may take weeks to obtain an isolate)
  • Requires specialized expertise
  • Low specificity, can be cross reactive
  • Low sensitivity
  • Must be cultivated within a eukaryotic host cell
  • Specialized reference laboratories only; not for routine diagnosis
  • Highly trained technician that can properly examine and interpret specific staining
  • Cell stocks routinely tested for Mycoplasma contamination by PCR
  • Positive results should be confirmed by an additional test, such as PCR
  • Commercially available kits
  • Quantitation possible
  • Lacks specificity
  • Multiple patient visits required to collect acute and convalescent paired sera specimens (time-sensitive sampling)
  • Time-consuming
  • No standardization or FDA approval
  • Not optimal for treatment decisions
  • No reference test for validating persistent infection
  • Clinical services: enzyme immunoassay (EIA) testing 2
  • CF, EIA and whole-inclusion fluorescence are not endorsed 3
  • Micro immunofluorescence (MIF) is the serological method of choice although interpretation is subjective 4
  • Diagnosis of acute infection based on single IgG titers is not recommended 4
  • Commercially available kits/platforms
  • High sensitivity and specificity
  • Rapid detection
  • Higher throughput
  • Greater discriminatory power
  • Provides information in time for a treatment decision
  • Variety of acceptable specimen types 1
  • Expensive
  • Requires specialized expertise and equipment
  • Clinical laboratories: real-time PCR using validated laboratory-developed test or commercially available FDA cleared multi-pathogen detection systems 2
  • CDC: Multiplex qPCR used for C. pneumoniae detection in NP, OP (throat) swab, sputum, tissue, or CSF 6
  • qPCR is the preferred method for the diagnosis of an acute C. pneumoniae infection 5

1 Acceptable specimen types vary by system but may include:

  • Combined nasopharyngeal (NP) and oropharyngeal (OP) swabs in viral transfer media (VTM) or universal transfer media (UTM)
  • NP swab in VTM/UTM
  • OP swab in VTM/UTM
  • NP aspirates
  • Sputum
  • Tissue
  • Bronchial lavage (BAL) fluid
  • Bronchial washings
  • Cerebrospinal fluid

2 State and local departments of public health may also offer these diagnostic tests for the detection of C. pneumoniae.

3 CF is not recommended for diagnosis of acute C. pneumoniae infection because of cross-reactivity with other Chlamydia species and other enteric bacteria. Also, the sensitivity for detecting reinfection is low. Whole-inclusion fluorescence tests are also not species-specific and have not been widely evaluated. EIA is not a recommended diagnostic method because of low sensitivity and specificity.

4 MIF is the only species-specific antibody test available that can measure isotype-specific antibody titers to all Chlamydia species simultaneously. However, MIF testing is technically complex and interpretation is subjective.

5 PCR has demonstrated greater utility for rapid and accurate detection of etiologies, especially in outbreak settings.

6 Culture can be performed at CDC but is not used for routine diagnostic purposes.

7 Refer to Standardizing Chlamydia pneumoniae assays: Recommendations from the Centers for Disease Control and Prevention (USA) and the Laboratory Centre for Disease Control (Canada)external icon for further recommendations.

CF – Complement fixation, EIA – enzyme immunoassay, MIF – microimmunofluorescence, qPCR – quantitative polymerase chain reaction, NP – nasopharyngeal, OP – oropharyngeal, CSF – cerebrospinal fluid


  • Benitez AJ, Thurman KA, Diaz MH, Conklin L, Kendig NE, Winchell JM. Comparison of real-time PCR and a microimmunofluorescence serological assay for the detection of Chlamydophila pneumoniae infection in an outbreak investigation. J Clin Micro. 2012;50(1):151–3.
  • Kumar S, Hammerschlag MR. Acute respiratory infection due to Chlamydia pneumoniae: Current status of diagnostic methods. Clin Infect Dis.2007;44:568–76.
  • Dowell SF, Peeling RW, Boman J, et al. Standardizing Chlamydia pneumoniae assays: Recommendations from the Centers for Disease Control and Prevention (USA) and the Laboratory Centre for Disease Control (Canada). Clin Infect Dis. 2001;33:492–502.