Laboratory diagnosis of respiratory infections
In our laboratory, we offer tests for the diagnosis of upper respiratory tract infections-pharyngitis, sinusitis, ocular and ear infections, and lower tract infections including pneumonia and bronchitis. Today we will focus on the diagnosis of common bacterial causes of pharyngitis and lower respiratory tract infections. Dr Miller will cover mycobacterial, fungal, and viral causes of lower respiratory tract infections with a special emphasis on the use of molecular methods to detect these organisms.
Upper respiratory tract infections
Pharyngitis- Group A streptococci is the most important bacterial cause of pharyngitis. Although ...view middle of the document...
Must be done by culture; molecular methods have not been validated.
Lower respiratory tract infections
Overview- Lower respiratory tract specimens are submitted to the laboratory for the diagnosis of airway infections including but not limited to community and hospital acquired pneumonia including ventilator associated pneumonia, bronchitis, chronic airway infection in cystic fibrosis patients, lung abscess, and tuberculosis. Specimen types submitted for the detection of etiology of these infections include: sputum, induced sputum, tracheal aspirates, non-bronchoscopic bronchoalveolar lavage (BAL) from intubated patients, and bronchoscopically obtained specimens including bronchial washes and BAL, and pleural fluid. Other specimens discussed in the literature but essentially never done at UNC Hospitals include transbronchial biopsy for detection of PCP, fungi, mycobacterium, and viruses; protected bronchial brush for anaerobic bacteria, fungi, viruses, transthoracic needle aspiration and open lung biopsy. Importantly only 60% of patients with CAP can produce sputum. Chest tube drainage is sometimes sent but we don’t know what to do with it.
1. Specimen quality determined by gram stain-
a. Sputum gram stain screening-ratio of WBC to epithelial cells as seen on low power field must be greater than 1. Screening is not done in cystic fibrosis patients (sputum producers almost always have purulent sputa and we are looking for a limited number of organisms); patients suspected of either M. tuberculosis or Legionella pneumophilia. Try to tell morphology and what it is consistent with. For example, Streptococcus pneumoniae has a distinctive morphology, lancet shaped diplococcus; we should report: gram positive, lancet shaped diplococci consistent with Streptococcus pneumoniae. Recent study of pneumococcal pneumonia showed 16% had inadequate specimens, gram stain was positive in 63% and culture in 86%.
Other organisms with distinctive gram stains include:
Gram positive cocci in clusters-Staphylococcus aureus
Thin gram negative rods- Pseudomonas aeruginosa
Pointed gram negative rods-Fusobacterium
Barnching, beaded gram positive rods- Nocardia
Mixed gram positive cocci and thin gram negative rods-mixed anaerobic infections
Pleiomorphic gram negative coccobacilli-Haemophilus
Gram negative diplococci-Moraxella
b. Tracheal aspirate screening-as per sputum with the additional proviso that the specimen must have organisms seen on oil immersion. Over 90% of specimens that have “no organisms seen” on gram stain will not grow a pathogen, so they are only cultured by request. Likewise, if a specimen shows only yeast, it too is not cultured because it is likely to represent endotracheal tube colonization which is common. Candida pneumonia is so rare that it needs to be diagnosed by other means as tracheal...