Community-acquired pneumonia (CAP) is pneumonia that is contracted in the community rather than in the hospital setting. CAP is a heterogeneous infection with a variety of potential causative pathogens and is associated with significant morbidity and mortality. The detection of an infiltrate on a chest radiograph is the standard for diagnosis of CAP, and because treatment is generally empiric, laboratory tests are not considered essential for most patients. However, laboratory tests are recommended for patients hospitalized due to severe CAP and for specific populations, such as those at risk for drug-resistant pathogens, whose treatment would be affected by microbiologic test results. Some laboratory tests used to evaluate patients with CAP include sputum culture and Gram stain, blood culture, urinary antigen testing, and polymerase chain reaction (PCR) testing of respiratory specimens.
For information concerning COVID-19, refer to the ARUP Consult COVID-19 topic. For information concerning hospital-acquired pneumonia, refer to the ARUP Consult Hospital-Acquired and Ventilator-Associated Pneumonia topic.
Quick Answers for Clinicians
Some of the primary bacterial pathogens associated with community-acquired pneumonia (CAP) are Streptococcus pneumoniae, Mycoplasma pneumoniae, Staphylococcus aureus, Legionella species, Chlamydia pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. Of note, bacterial pathogens can coexist with viral pathogens and it is difficult to rapidly determine whether CAP is solely of viral origin; for that reason, the Infectious Diseases Society of America (IDSA) and American Thoracic Society (ATS) recommend initial empiric treatment for potential bacterial infection or coinfection in patients who present with CAP.
Risk factors for drug-resistant pathogens such as methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa, or similar multidrug-resistant Gram-negative bacteria in patients with community-acquired pneumonia (CAP) include previous identification of these organisms (particularly in respiratory tract specimens), recent hospitalization, and treatment with parenteral antibiotics. Refer to Laboratory Testing for specific testing recommendations.
The Infectious Diseases Society of America (IDSA) and American Thoracic Society (ATS) recommend proceeding with empiric antibiotic treatment in patients with clinically suspected, radiographically confirmed community-acquired pneumonia (CAP), irrespective of procalcitonin test results. Serum procalcitonin levels have been investigated as a means to differentiate between viral and bacterial pneumonia, given that bacterial etiologies have been associated with higher procalcitonin concentrations, but a cutoff level to differentiate between viral and bacterial illness has not been established. Therefore, procalcitonin levels are not recommended to determine whether to proceed with antibiotic treatment. Serial procalcitonin concentrations are also not generally recommended to determine treatment duration; procalcitonin levels may not be increased in patients with bacterial/viral coinfection or in cases of pneumonia caused by Legionella or Mycoplasma spp. The IDSA recommends use of clinical characteristics instead to assess patient improvement and stability (eg, vital signs, ability to eat, normal mentation). Measurement of procalcitonin is also not recommended in pediatric outpatients with CAP but may be useful in cases of severe illness for clinical management or to gauge treatment response.
Indications for Testing
Laboratory testing has a limited role in the diagnosis of patients with CAP. Diagnosis is often based on clinical features and/or chest radiography. Current testing cannot rapidly and accurately confirm the presence of only viral pathogens at presentation; therefore, treatment does not depend on microbiologic test results but is generally empiric to cover the possibility of potential coinfection or bacterial infection. However, laboratory testing is recommended for specific patient populations with CAP, such as those with severe CAP or with risk factors for methicillin-resistant Staphylococcus aureus (MRSA) or Pseudomonas aeruginosa infection, for whom results will impact treatment.
The following table summarizes circumstances in which specific tests are indicated; refer to the sections that follow for additional information.
|Testing Method||Circumstances for Testing (Adults)||Circumstances for Testing (Childrena)|
Current empiric treatment for MRSA or P. aeruginosa infection
Positive nasal screening result for MRSA
Hospitalization and parenteral antibiotics within previous 3 mosb
Failure to improve clinically or clinical decline after start of antibiotic treatment
Hospitalized with moderate, severe, or complicated CAP
S. aureus-caused bacteremia (repeat blood cultures to confirm bacteremia has resolved)
|Sputum Gram stain and culture||
Intubation (note: endotracheal aspirates are preferred to sputum in patients being intubated)
Current empiric treatment for (or history of) MRSA or P. aeruginosa infection
Hospitalization and parenteral antibiotics within previous 3 mosb
Positive nasal screening result for MRSA
|Hospitalized with CAP (if able to provide a sputum sample)|
|Gram stain and culture of lower respiratory tract specimens (eg, endotracheal aspirates)||
Severe CAP with intubation
For Legionella spp. (culture): severe CAP, unless PCR is being performed
|Gram stain and culture of pleural fluid||If pleural fluid specimen is collected||If pleural fluid specimen is collected|
|Urinary antigen tests||For Streptococcus pneumoniae: severe CAP
For Legionella spp.: severe CAP or epidemiologic factors that increase risk of Legionella infection
|Not recommended for diagnosis of pneumococcal pneumonia in children because results are often false positive|
|PCR for influenza||Any case of CAP in an adult during seasons of increased influenza activity||Any case of CAP in a child|
|PCR for other respiratory viruses||Hospitalization with suspected CAP when case is categorized as severe or patient is immunocompromised||Any case of CAP in a child|
|PCR for other pathogens (eg, Mycoplasma pneumoniae, Legionella spp., Chlamydophila pneumoniae)||Consider to help guide antimicrobial therapy when clinically indicated||M. pneumoniae testing: consider to help guide antimicrobial therapy when clinically indicated|
|Nasal PCR for MRSA||MRSA risk factors (severe CAP, history of MRSA or P. aeruginosa infection, previous hospitalization and treatment with parenteral antibiotics)||—|
|NGS||Not currently recommended by guidelines but holds promise||Not currently recommended by guidelines but holds promise|
aThese recommendations apply to infants and children >3 months of age.
bThis recommendation applies even if the antibiotics were administered outside of the hospital setting.
NGS, next generation sequencing
The diagnostic contribution of blood cultures is limited for most patients with CAP. The Infectious Diseases Society of America (IDSA) and American Thoracic Society (ATS) discourage the routine use of blood cultures in both adult outpatients and hospitalized patients with CAP, except in the circumstances noted in the table above. In these cases, blood culture results may influence whether treatment should be adjusted or deescalated.
Blood cultures (along with sputum cultures) are recommended in adult patients with positive nasal screening results for MRSA. (See Polymerase Chain Reaction Tests below.)
The IDSA and the Pediatric Infectious Diseases Society (PIDS) recommend blood cultures in pediatric patients (infants and children older than 3 months) in the circumstances outlined in the table above.
Sputum Gram Stain and Culture
Sputum evaluation has been shown to have limited utility in detecting causative organisms for CAP. A valid sputum specimen can be difficult to obtain, and test performance varies by organism and whether antibiotics were administered. Although the IDSA and ATS discourage the routine use of sputum Gram stain and culture in adult outpatients with CAP, this testing is recommended before treatment in the circumstances described in the table above. Sputum Gram stain and culture results may influence whether treatment should be adjusted or deescalated in these circumstances.
Sputum cultures (along with blood cultures) are also recommended in adult patients with positive nasal screening results for MRSA. (See Polymerase Chain Reaction Tests below.)
Gram Stain and Culture of Lower Respiratory Tract Specimens
In all patients with CAP who must be intubated, Gram stain and culture of lower respiratory tract specimens, such as endotracheal aspirates, should be performed soon after intubation. The likelihood of MRSA or P. aeruginosa-associated pneumonia is higher in these patients, and endotracheal aspirates demonstrate a greater microbiologic yield than do sputum cultures.
Gram Stain and Culture of Pleural Fluid
For pediatric patients older than 3 months with CAP, the IDSA and PIDs recommend Gram stain and culture of any pleural fluid specimen obtained. Pleural fluid specimens can also be tested using PCR. (Refer to Polymerase Chain Reaction Tests below.)
Urinary Antigen Tests
Urinary antigen testing can be used as an alternative method to identify Legionella species and S. pneumoniae. However, urinary antigen testing for S. pneumoniae is not recommended for routine use in patients with CAP, except in cases of severe CAP.
Use of this testing for Legionella spp. is recommended only in those with severe CAP or with epidemiologic factors that increase the risk of Legionella infection (eg, recent travel or potential exposure during a Legionella outbreak). Urinary Legionella antigen testing should be performed in conjunction with culture or a PCR (nucleic acid amplification test [NAAT]) of lower respiratory tract secretions for Legionella in patients with severe CAP.
Inflammatory Marker Tests
Bacterial etiologies have been associated with higher serum procalcitonin concentrations, but a cutoff level to distinguish viral from bacterial illness has not been established. Therefore, the IDSA and ATS do not recommend use of procalcitonin levels to determine whether to initiate antibiotic treatment. In addition, serial procalcitonin concentrations are not generally recommended to determine treatment duration; procalcitonin levels may not be increased in patients with bacterial/viral coinfection or in cases of pneumonia caused by Legionella or Mycoplasma spp.
C-reactive protein (CRP) levels may be useful to either support or rule out the diagnosis of CAP. CRP levels >30 mg/L, in conjunction with clinical signs and symptoms associated with pneumonia, support a CAP diagnosis. In patients with an acute cough lasting <3 weeks, CRP levels <10 mg/L, or between 10 and 50 mg/L in the absence of fever or dyspnea, do not support a diagnosis of CAP.
The IDSA and PIDs do not recommend the use of inflammatory marker testing for pediatric outpatients with CAP, but suggest that in cases of severe illness, these tests may be useful to aid in clinical management and to gauge treatment response.
Polymerase Chain Reaction Tests
A rapid influenza PCR is recommended in adult patients with CAP during seasons of increased influenza activity but is not essential when few influenza cases are being reported. Tests for influenza and other respiratory viruses are recommended in pediatric patients with CAP. Refer to the ARUP Consult Influenza topic for guidance about recommended testing.
Although PCR testing for other respiratory viruses is not recommended for adults in an outpatient setting, the ATS recommends this testing in hospitalized adults with suspected CAP who are immunocompromised or whose illness is categorized as severe. For a list of criteria for severe CAP, refer to the ATS clinical guidelines.
PCR tests for pathogens such as M. pneumoniae, Legionella spp., and C. pneumoniae can be considered to help guide empiric therapy when clinically indicated (eg, in patients with severe CAP, either culture of lower respiratory tract specimens or PCR for Legionella is recommended). Acceptable specimen types for these tests include bronchoalveolar lavage (BAL), bronchial brushings, nasopharyngeal swab, sputum, tracheal aspirates, or pleural fluid.
Nasal Swab for MRSA
Nasal PCR offers high specificity and negative predictive value (NPV) for MRSA pneumonia. In the absence of nasal colonization, MRSA pneumonia is unlikely. Coverage for MRSA pneumonia can often be suspended when the results of nasal swab testing are negative, particularly when CAP is not severe. Nasal culture for MRSA is associated with the same high specificity and NPV and may be less costly than PCR, but PCR yields results more rapidly.
The positive predictive value (PPV) is low for nasal swab testing. If results are positive, the patient should begin treatment for MRSA pneumonia, but the nasal swab results should be confirmed using blood and sputum cultures. If blood and sputum cultures are negative, MRSA treatment can generally be discontinued, or, in critically ill patients, deescalated.
Next Generation Sequencing
Risk stratification calculators are often used to evaluate illness severity in patients with CAP and make determinations about inpatient versus outpatient treatment. The IDSA and ATS recommend use of the Pneumonia Severity Index (PSI), which evaluates patients for 20 risk factors. Laboratory tests necessary for PSI assessment include arterial pH, blood urea nitrogen (BUN), sodium, glucose, and hematocrit tests, in combination with other clinical and radiographic findings.
Patient assessment based on the IDSA/ATS major and minor criteria defined in 2007, rather than the PSI or other calculators, is recommended to determine intensive care unit (ICU) admission. Laboratory parameters included among the criteria are BUN level, white blood cell (WBC) count, and platelet count. Complete criteria are described in the 2019 IDSA/ATS CAP guideline.
Procalcitonin and CRP can be used in more severe cases of CAP in pediatric patients, in conjunction with clinical findings, to evaluate response to treatment. The IDSA and ATS recommend that an assessment of clinical stability, including factors such as vital signs, ability to eat, and normal mentation, rather than serial procalcitonin measurements, be used to guide therapy duration.
Testing to determine antibiotic levels in serum can also be used to help optimize antibiotic concentrations and dosing (refer to the ARUP Consult Therapeutic Drug Monitoring topic for testing details).
ARUP Laboratory Tests
(Note: Primary microbiology tests should be performed as close to the patient as possible.)
Direct Fluorescent Antibody (DFA) Stain/Cell Culture
Qualitative Polymerase Chain Reaction
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