Laboratory diagnosis of lower respiratory tract infections; Key points

This post was most recently updated on November 28th, 2018

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 expectorated sputum is always best for bacterial 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 the detections of pathogen causing lower respiratory tract infections. Selection of a particular method depends on the clinical presentation as per the request of physician.
   

   If a few colonies of Gram-negative rods are isolated from the sputum or throat swab of a hospitalized patient, further identification and anti-microbial susceptibility testing are of no clinical relevance, since neither procedure will have any effect on treatment of the patient.

   

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 the 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 immunocompromised 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. NAATs have largely replaced rapid antigen tests and culture for respiratory virus detection.
10. Calcium alginate swabs are not acceptable for nucleic acid amplification testing.
11. Bronchoscopy with washings is the optimal diagnostic specimen in paediatrics.

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