Recommendations for the microbiological investigation of community acquired pneumonia (CAP)
| Pneumonia severity (based on clinical judgement supported by severity scoring tool) | Treatment site | Preferred microbiological tests |
| Low severity (eg, CURB65 = 0–1 or CRB-65 score = 0, <3% mortality) | Home | None routinely.PCR, urine antigen or serological investigations* may be considered during outbreaks (eg, Legionnaires’ disease) or epidemic mycoplasma years, or when there is a particular clinical or epidemiological reason. |
| Low severity (eg, CURB65 = 0–1, <3% mortality) but admission indicated for reasons other than pneumonia severity (eg, social reasons) | Hospital | None routinelyPCR, urine antigen or serological investigations* may be considered during outbreaks (eg, Legionnaires’ disease) or epidemic mycoplasma years, or when there is a particular clinical or epidemiological reason. |
| Moderate severity (eg, CURB65 = 2, 9% mortality) | Hospital | Blood cultures (minimum 20 ml) |
| Sputum for routine culture and sensitivity tests for those who have not received prior antibiotics (±Gram stain*) | ||
| Pneumococcal urine antigen test | ||
| Pleural fluid, if present, for microscopy, culture and pneumococcal antigen detection | ||
| PCR or serological investigations* may be considered during mycoplasma years and/or periods of increased respiratory virus activity. | ||
| Where legionella is suspected¶, investigations for legionella pneumonia: | ||
| (a) urine for legionella antigen | ||
| (b) sputum or other respiratory sample for legionella culture and direct immunofluorescence (if available). If urine antigen positive, ensure respiratory samples for legionella culture | ||
| High severity (eg, CURB65 = 3–5, 15–40% mortality) | Hospital | Blood cultures (minimum 20 ml) |
| Sputum or other respiratory sample‡ for routine culture and sensitivity tests (±Gram stain†) | ||
| Pleural fluid, if present, for microscopy, culture and pneumococal antigen detection. | ||
| Pneumococcal urine antigen test | ||
| Investigations for legionella pneumonia: | ||
| (a) Urine for legionella antigen | ||
| (b) Sputum or other respiratory sample‡ for legionella culture and direct immunofluorescence (if available) | ||
| Investigations for atypical and viral pathogens:** | ||
| (a) If available, sputum or other respiratory sample for PCR or direct immunofluorescence (or other antigen detection test) for Mycoplasma pneumoniae Chlamydia spp, influenza A and B, parainfluenza 1–3, adenovirus, respiratory syncytial virus, Pneumocystis jirovecii (if at risk) | ||
| (b) Consider initial and follow-up viral and “atypical pathogen” serology§ |
*If PCR for respiratory viruses and atypical pathogens is readily available or obtainable locally, then this would be preferred to serological investigations.
†The routine use of sputum Gram stain is discussed in the text.
‡Consider obtaining lower respiratory tract samples by more invasive techniques such as bronchoscopy (usually after intubation) or percutanous fine needle aspiration for those who are skilled in this technique.
§The use of paired serology tests for patients with high severity CAP is discussed in the text. If performed, the date of onset of illness should be clearly indicated on the laboratory request form.
¶Patients with clinical or epidemiological risk factors (travel, occupation, comorbid disease). Investigations should be considered for all patients with CAP during legionella outbreaks.
**For patients unresponsive to β-lactam antibiotics or those with a strong suspicion of an “atypical” pathogen on clinical, radiographic or epidemiological grounds.