The commonest infections are acute tracheo-bronchitis, acute exacerbations of chronic bronchitis, and the pneumonias. in many or most cases the primary infection is caused by a virus, e.g. rhinovirus, myxovirus. adenovirus or respiratory syncytial virus, but there is often a secondary infection with a bacterial pathogen from the nasopharynx, most commonly Pneumococcus or Haemophilus influenzae. Pneumococcus also appears to be the primary cause of many cases of pneumonia, particularly lobar pneumonia, but often these pneumonic infections are triggered by a preceding viral infection of the upper respiratory tract, such as the common cold. Other secondary invaders of the lower tract include Staphylococcus aureus, which may cause fatal pneumonia after influeanza, coliform bacilli and Pseudomonas aeruginosa, Branhamella cararrhalis, Candida albicans and Aspergillus fumigauss. The staphylococcus, coliforms and candida are found particularly in hospitalized patients treated with antibiotics to which these organisms are resistant.
Other organisms that may cause primary infection in the bronchial tract or lungs are Mycoplasma pneumoniae, which is the commonest, Legionella pneumnophila, Chlamydia psittaci B and Coxtella burnefi. The protozoon Pneumocystis carini is liable to cause diffuse infection of the lungs in persons who are immunosuppressed or immunodeficient, e.g. patients infected with human immunodeficiency virus.
Identification of a viral pathogen is attempted only occasionally, as when the information is required for epidemiological purposes or the diagnosis of an obscure infection. Laboratory diagnosis is employed mainly for the identification of other, particularly bacterial pathogens, which may be susceptible to treatment with an antibiotic chosen with the knowledge of their identity.
In suspected pneumonia and other severe infections it is usual to start antibiotic therapy without waiting for the results of laboratory tests, and as pneumococcus and haemophilus are the likeliest bacterial pathogens, the blindly chosen drug is generally ampicillin, amoxicillin, augmentin or cotrimoxazole. though erythromycin or tetracycline should be substituted if failure of response or the clinical features suggest that the infection may be due to a β-lactamase-producing haemophilus or a mycoplasma or legionella. and flucloxacillin should be added if S. aureus may be the cause. As the drugs so chosen may still be inappropriate. laboratory identification of the causal organism should always be attempted at the earliest possible stage. For the best chance of success, specimens of sputum and blood for culture should be collected before the start of any antibiotic therapy. In suspected atypical pneumonia an initial blood sample for serology should be taken at the same early stage.
Specimens
Sputum. The material from lower respiratory infections most commonly submitted for bacteriological examination is sputum, a mixture of bronchial secretion and inflammatory exudates coughed up into the mouth and expectorated. There are, however, difficulties both in collecting a suitable sample and in interpreting the results of its culture. In some infections, e.g. those due to Mycoplasma or Legionella, there is often a lack of secretion and sputum cannot be obtained.
Sputum from a bacterial infection is purulent, containing yellow or green opaque material as well as clear mucoid secretion. Staff collecting specimens should be instructed in how to obtain and recognize the correct material. Many patients tend to swallow their sputum when it is coughed into the throat and, when asked to spit some out, may expectorate mainly saliva. Saliva can be recognized because it is relatively clear and is watery rather than viscous.
Busy or uninstructed staff may send such collections of saliva to the laboratory, but they should not be examined, for the results are likely to be misleading. Thus, the specimen may fail to yield a culture pathogen in the lower tract and may give growth of an irrelevant potential pathogen that is carried in the throat. Any salivary specimen should therefore be discarded and a report send to the physician stating that the specimen was mainly saliva and thus unsuitable for examination. The regular practice of rejecting unsuitable specimens usually induces staff in wards and clinics to take greater care in the collection procedure.
The decision to reject specimens should not be left to junior staff and clear criteria for rejection should be laid down for general application. Preferably the criteria should be based on a microscopical as well as a naked-eye assessment. Thus, if a Gram-stained smear of a homogenized specimen shows less than 10 polymorphs to every squamous epitheial cell, and the patient is not leucopenic, the material probably consists mainly of saliva.
Instructions for collecting sputum should include the following advice.
1. Make the collection in a disposable, wide-mouthed screw-capped plastic container of about 100 ml capacity.
2. If possible collect the sputum before any antibiotic therapy is begun, and when the patient first coughs on waking in the morning.
3. Instruct the patient to wait until he feels materia1 coughed into his throat and then to work it forward into his mouth and spit it directly into the opened container, trying to avoid spilling over the rim. At once tightly screw on the cap of the container. Wipe off any spilled material on its outside with a tissue moistened with disinfectant, but take care not to let any disinfectant enter the container.
4. If the patient has difficulty in coughing sputum into his mouth, ask a physiotherapist to pummel his chest. This exercise often causes exudates to move in the bronchi and stimulate productive coughing.
5. Deliver the specimen to the laboratory as quickly as possible, preferably within 2h, for delicate pathogens such as Pneumococcus and Haemophilus may die out during any longer delay.
Bronchial swabs and aspirates. The principal difficulty in sputum examinations arises from the inevitable mixing of the expectorated specimen with throat secretion and saliva. It thus becomes contaminated with hardy mouth commensal bacteria that may overgrow the more delicate lung pathogens, and often also with potential lung pathogens, such as pneumococcus and haemophilus, which are commonly carried in the throat. When found, the latter may be wrongly thought to have been infecting the lower respiratory tract.
This confusing contamination can be avoided if a specimen of bronchial secretion is collected by some means that prevents its contact with the throat and mouth. Such collection may be done by transtracheal puncture and aspiration or by the use of a protected swab passed through a bronchoscope into the bronchi. Direct aspiration of secretion through a bronchoscope, e.g. by bronchial lavage, is unsatisfactory as the inside of the bronchoscope is liable to become soiled with throat secretion.
However transtracheal aspiration and bronchial swabbing require anaesthesia of the patient and the attention of skilled medical staff, and for these reasons are generally not performed. Nevertheless they may be attempted for the diagnosis of unusual or obscure infections.
Blood culture. In all cases of suspected pneumonia a sample of blood should be taken for culture before antibiotics are given. Lung infections are commonly associated with bacteriaemia and it may be possible to culture from the blood a delicate pathogen whose growth is suppressed in cultures of sputum contaminated with salivary organisms. Moreover, the finding of a bacterium in the blood is strong evidence that it has been infecting the lungs and is not merely a throat organism contaminating sputum.
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