Doing some pneumonia CME and had a quick question. Why is a specific pathogen often not isolated/identified in the hospitalized patient with community acquired pneumonia? I was thinking maybe the amount and diversity of microorganisms in the lungs make it difficult to tell who the main player is in the infection?
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A lot of “CAP” syndromes are actually caused by viruses.
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It’s often not necessary to identify a specific pathogen, as knowledge of the typical microbiology of community acquired pneumonia in the general population leads to very effective empiric antimicrobial selection. In other words, knowing the most common causes informs our “best guess” antibiotics that successfully treat it the vast majority of the time.
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Tests have limited sensitivity to “catch” these organisms. For example, getting a high quality, non-contaminated sputum sample is tricky, and then a bacteria needs to be grown in culture – which not all bacteria are easily cultured. The bug then needs to be identified and tested for antibiotic susceptibilities … which takes a few days. The patient often does not need to be hospitalized that long, and may well already be discharged and feeling better by the time such cultures are finalized in many (but certainly not all) situations.
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PCR tests have improved our ability to “catch” particular pathogens, but in many situations don’t actually end up changing what we do with the person – see #1, as our “best guess” antibiotics are often quite good. Culture and/or PCR testing becomes more useful and important when people are critically ill, immunocompromised, or have other risk factors for unusual or drug-resistant organisms.
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That all makes sense. Thank you!