Introduction

Aetiological diagnoses in respiratory tract infections may be achieved by identifying the causative agent, antigenic subcellular products or specific nucleic acid sequences from that agent present in material from the infectious site. The aetiology may also be demonstrated by the finding of an antibody response to the infectious agent.

The process of diagnosing respiratory infections is complicated by the great diversity of microbial agents involved. Hence, a multitude of different methods for the identification of different types of bacteria, viruses, fungi, protozoa and helminths are available, and the problem of choosing the appropriate tests in the clinical setting at hand is often significant. Although diagnostic efforts may be limited because of the trivial nature of the infection or the availability of reasonably effective empirical therapy, an aetiological diagnosis is often indicated.

In addition to the great variety of microbial agents of potential importance in airway infections, a further problem is the existence of an abundant indigenous bacterial flora of the oral cavity, posing difficulties for obtaining uncontaminated specimens. It is often difficult to conclude whether identified microbial agents are the cause of an ongoing infectious process or merely colonisers of the oropharynx. For most viral agents as well as for Legionella pneumophila, Mycobacterium tuberculosis, Pneumocystis carinii and pathogenic dimorphic fungi the mere identification of the respective agent in respiratory tract secretions is considered to be a proof of ongoing disease with that agent.