Laboratory diagnosis of lower respiratory tract infections; Key points

This post contains fundamental and key points regarding laboratory diagnosis of lower respiratory tract infections  (LRTI) so will be helpful for the revision.

1. First morning sputum is always best for culture. Expectorated sputum has been the primary means of determining the causes of lower respiratory tract infections. Induced sputum, endotracheal or tracheotomy suction specimen, transtracheal aspirates are also used. Sometime sample can be obtained using  bronchoscopy e.g. bronchial washings, aspirates, bronchoalveolar lavage (BAL).
2. Direct visual examinations of Lower respiratory specimens: KOH preparation or periodic acid-schiff-stained smears for fungal element detection, Gram staining (for bacteria and yeasts), Ziehl Neelsen staining for Mycobacterium tuberculosis (or Kinyoun carbolfuchsin stain, Auramine or auramine-rhodamine) is commonly used  direct examination methods for direct examination of lower respiratory specimens depending on the clinical presentation or  as per the request of physician.

   

3. Culture of Respiratory tract sample: Common etiologic agents of lower respiratory tract infections will be isolated on routinely used media: 5% Sheep blood agar, MacConkey agar (for isolation and differentiation of gram negative bacilli), and chocolate agar (for Haemophilus and Neisseria spp). For suspected cases of legionnaires’ disease, Buffered charcoal-yeast extract agar  (BCYE) and for tuberculosis, Lowenstein Jensen medium is used.
4. Blood cultures that accompany sputum specimens may occasionally be helpful, particularly in high risk community acquired pneumonia patients.
5. The laboratory should be contacted for specific instructions prior to collection of specimens for fastidious pathogens such as Bordetella pertussis.
6. The range of pathogens causing exacerbations of lung disease in cystic fibrosis patients has expanded and specimens for mycobacterial and fungal cultures should be collected in some patients.
7. In the immuno-compromised host, a broad diagnostic approach based on invasively obtained specimens is suggested.
8. Most negative rapid antigen test results should be confirmed by another method.
9. Calcium alginate swabs are not acceptable for nucleic acid amplification testing.

List of Bacteria causing Respiratory Tract infection

1. Definitive pathogens
   1. Bordetella pertusis
   2. Chlamydia trachomatis
   3. Chlamydophila pneumonia
   4. Mycoplasma pneumonia
   5. Mycobacterium tuberculosis
   6. Corynebacterium diphtheria (toxin-producing)
   7. Legionella spp

B: Possible pathogens

1. Streptococcus pneumoniae
2. Staphylococcus aureus
3. Neisseria meningitidis
4. Haemophilus influenzae
5. Haemophilus parainfluenzae
6. Pseudomonas spp
7. Enterobacteriaceae
8. Moraxella catarrhalis

List of fungal pathogens causing lower respiratory tract infections

1. Pneumocystis jiroveci (Pneumocystis carinii)
2. Nocardia spp
3. Histoplasma capsulatum
4. Coccidioides immitis
5. Cryptococcus neoformans (may also be recovered from patients without disease)
6. Blastomyces dermatitidis