Lab Diagnosis of Lower Respiratory Tract Infections

Streptococcus pnuemoniae: Gram positive diplococci

Last updated on June 21st, 2021

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

Streptococcus pnuemoniae: Gram positive diplococci

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 tracheostomy suction specimen, transtracheal aspirates are also used. Sometimes samples can be obtained using bronchoscopy e.g. bronchial washings, aspirates, bronchoalveolar lavage (BAL).

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 the treatment of the patient.

Culture of Respiratory tract sample: Common etiologic agents of lower respiratory tract infections will be isolated on routinely used media: 5% Sheep blood agarMacConkey 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.

Streptococcus pneumoniae with optochin sensitivity
Optochin sensitive colonies of S. pneumoniae
  • Blood cultures that accompany sputum specimens may occasionally be helpful, particularly in high-risk community-acquired pneumonia patients.
  • The laboratory should be contacted for specific instructions prior to the collection of specimens for fastidious pathogens such as Bordetella pertussis.
  • 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.
  • In the immunocompromised host, a broad diagnostic approach based on invasively obtained specimens is suggested.
  • Most negative rapid antigen test results should be confirmed by another method.NAATs have largely replaced rapid antigen tests and culture for respiratory virus detection.
  • Calcium alginate swabs are not acceptable for nucleic acid amplification testing.
  • Bronchoscopy with washings is the optimal diagnostic specimen in pediatrics.

List of Bacteria causing Respiratory Tract Infection

  1. Definitive pathogens
    1. Bordetella pertussis
    2. Chlamydia trachomatis
    3. Chlamydophila pneumonia
    4. Mycoplasma pneumoniae
    5. Mycobacterium tuberculosis
    6. Corynebacterium diphtheriae (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

About Acharya Tankeshwar 474 Articles
Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. I am working as an Asst. Professor and Microbiologist at Department of Microbiology and Immunology, Patan Academy of Health Sciences, Nepal. If you want me to write about any posts that you found confusing/difficult, please mention in the comments below.

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