Acute pneumonias occur in a variety of clinical settings and accurate identification of bacterial causes is extremely important. No microbiological tool is either 100 % sensitive or 100 % specific, and despite investigations, aetiology remains unanswered in more than 30 % of pneumonia. No sample may be necessary for patients treated as outpatients, non invasive respiratory specimens are preferred in hospitalised individuals (community or healthcare associated), while invasive specimens are used as second line for community acquired pneumonia (CAP) in intensive care, and in the first line where pneumonia occurs in immunosuppressed patients. Bacterial cultures have an important place, if the sample is taken before the introduction of antibiotic therapy. Some contexts may justify the use of blood cultures, testing for urinary antigens or serology. PCR is already becoming available as a daily service but the short-term future probably belongs to molecular multiplex panels capable of detecting many microorganisms within hours, especially in severe CAP resuscitation and in pneumonia in the immunosuppressed. High-throughput sequencing nucleotide techniques will soon revolutionize microbiological diagnosis in respiratory medicine, as in other areas of infectious diseases.
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