# Microbiological Testing in Community-Acquired Pneumonia — ATS/IDSA 2019

## General Principles

The 2019 ATS/IDSA guideline provides specific recommendations on when to obtain microbiological studies based on treatment setting and severity. The overall goal is to identify the causative pathogen for targeted therapy and appropriate de-escalation.

## Gram Stain and Sputum Culture

### Outpatients

- **Recommendation:** Do NOT routinely obtain sputum Gram stain and culture in outpatients with CAP (Conditional recommendation, Very low quality of evidence).
- **Rationale:** The yield is low, results rarely change management in outpatients, and empiric therapy is highly effective for most outpatient CAP.

### Inpatients

- **Recommendation:** Obtain pretreatment sputum Gram stain and culture in adults with CAP who:
  1. Are classified as having severe CAP (especially if intubated) (Conditional recommendation, Very low quality of evidence)
  2. Are being empirically treated for MRSA or P. aeruginosa (Strong recommendation, Very low quality of evidence)
  3. Were previously infected with MRSA or P. aeruginosa (particularly prior respiratory tract isolation)
  4. Were hospitalized AND received parenteral antibiotics in the last 90 days

- **Rationale:** Sputum cultures are essential when empiric coverage for resistant pathogens is initiated, to enable de-escalation at 48 hours based on culture results.

## Blood Cultures

### Outpatients

- **Recommendation:** Do NOT routinely obtain blood cultures in outpatients with CAP (Conditional recommendation, Very low quality of evidence).

### Inpatients

- **Recommendation:** Obtain pretreatment blood cultures in adults with CAP who:
  1. Are classified as having severe CAP (Conditional recommendation, Very low quality of evidence)
  2. Are being empirically treated for MRSA or P. aeruginosa (Strong recommendation, Very low quality of evidence)
  3. Were previously infected with MRSA or P. aeruginosa
  4. Were hospitalized AND received parenteral antibiotics in the last 90 days

- Do NOT routinely obtain blood cultures in nonsevere inpatient CAP without risk factors for MRSA or P. aeruginosa (Conditional recommendation, Very low quality of evidence).

## Urinary Antigen Testing

### Legionella Urinary Antigen

- **Recommendation:** Do NOT routinely test for Legionella urinary antigen in adults with CAP (Conditional recommendation, Low quality of evidence).
- **Test when:**
  - Epidemiological factors suggest Legionella (e.g., association with a Legionella outbreak)
  - Recent travel involving hotel or cruise ship stay
  - Severe CAP requiring ICU admission
- **Limitation:** The Legionella urinary antigen detects only L. pneumophila serogroup 1 (accounts for approximately 80% of community-acquired Legionella infections).

### Pneumococcal Urinary Antigen

- **Recommendation:** Do NOT routinely test for Streptococcus pneumoniae urinary antigen in adults with CAP (Conditional recommendation, Low quality of evidence).
- **Test when:**
  - Severe CAP requiring ICU admission
- **Rationale:** A positive test may allow narrowing of therapy from broad-spectrum to targeted anti-pneumococcal coverage.

## Influenza Testing

- **Recommendation:** Test for influenza with a rapid molecular assay (e.g., RT-PCR) — preferred over rapid antigen detection tests — in adults with CAP when influenza viruses are circulating in the community (Conditional recommendation, Low quality of evidence).
- **Rationale:** Identification of influenza informs antiviral therapy and infection control decisions.
- Molecular assays (RT-PCR) are strongly preferred due to higher sensitivity compared with rapid antigen detection tests.

## Procalcitonin

- **Recommendation:** Do NOT use initial procalcitonin levels to determine whether to initiate antibiotic therapy in adults with clinically suspected and radiographically confirmed CAP (Strong recommendation, Moderate quality of evidence).
- **Key point:** If clinical evaluation and chest imaging support a diagnosis of CAP, empiric antibiotics should be started regardless of procalcitonin level. Procalcitonin should not delay or withhold antibiotic therapy.
- **Rationale:** Available evidence does not support withholding antibiotics in radiographically confirmed CAP based on low procalcitonin. The guideline acknowledges that procalcitonin may play a role in guiding duration of therapy, but this was not the focus of the recommendation.

## De-escalation Strategy

- When empiric coverage for MRSA or P. aeruginosa is initiated, microbiological data should be used to de-escalate therapy.
- **At 48 hours:**
  - If cultures are negative for MRSA: discontinue vancomycin or linezolid.
  - If cultures are negative for P. aeruginosa: de-escalate to standard CAP regimen.
  - A negative MRSA nasal PCR has high negative predictive value and supports safe discontinuation of empiric MRSA coverage.
- Continued empiric coverage without culture data to justify it is not recommended (Strong recommendation, Low quality of evidence).

## Limitations

- Sputum cultures have variable sensitivity and specificity depending on specimen quality and prior antibiotic exposure.
- Blood culture positivity in CAP is low (approximately 5-14% in hospitalized patients), but when positive, results significantly influence management.
- Urinary antigen tests have high specificity but may remain positive for weeks after infection, limiting their use in patients with recent pneumonia.
