Lung biopsy

There are three major lung biopsy specimen types that may be received in the laboratory.

Open lung biopsy (sometimes labeled “Thoracoscopic”)

This specimen usually consists of a wedge of lung tissue obtained during surgery and submitted in a clean, sterile container.

Trans-thoracic needle biopsy

These specimens are taken by pushing a small bore needle through the chest wall into the lung and aspirating the contents of the needle into a small amount of fluid.

Trans-bronchial lung biopsy

These specimens are taken using a fiberoptic bronchoscope and removing a portion of lung tissue. A much smaller piece of tissue is obtained than with open lung biopsy.


Direct Examination

Prepare smears for:

  • Gram stain
  • KOH Calcoflour stain
  • Auramine stain
  • 1 extra smear for potential special stains


Media Incubation
Blood Agar (BA) CO2, 35°C x 48 hours
Chocolate Agar (CHOC) CO2, 35°C x 48 hours
MacConkey Agar (MAC) O2, 35°C x 48 hours
Wilkins Chalgren Agar (WC) AnO2, 35°C x 48 hours
WC Nalidixic acid – Tween 80 (NAT) AnO2, 35°C x 48 hours
WC Nalidixic acid – Vancomycin (NAV) AnO2, 35°C x 48 hours
Thioglycolate broth (THIO) O2, 35°C x 48 hours
Sabouraud’s Heart Infusion Agar (SABHI) O2, 30°C x 4 weeks
SABHI with Chloramphenicol (SABHI-C) O2, 30°C x 4 weeks

If B. cepacia is requested or specimen is from a patient with Cystic Fibrosis, add:

*Burkholderia cepacia* Agar (BC) O2 35°C x 3 days

Keep the BA, CHOC and MAC plates CO2 35°C x 3 days

If Nocardia is requested, add:

Vancomycin Colistin Nalidixic acid (VCN) CO2 35°C x 5 days

Interpretation Examine aerobic plates after 24 and 48 hours incubation and anaerobic plates after 48 hours incubation for any growth and identify all isolates including yeast.

If no growth on aerobic and anaerobic plates, but organisms resembling anaerobic organisms are seen on Gram stain, re-incubate the WC, NAT, NAV and THIO for an additional 48 hours.

Examine the BC plate daily for 3 days.


Direct Examination

Gram Stain
Report with quantification.

KOH Calcofluor Stain
Report fungal elements seen or not seen.

Report acid-fast bacilli with quantification or acid-fast bacilli not seen.


Negative Report

  • “No growth.”
  • “No B. cepacia isolated” if B. cepacia culture is requested.
  • “No Nocardia isolated” if Nocardia culture is requested.

Positive Report

  • Report all isolates with appropriate susceptibilities.
  • Telephone all positive results of direct examination and culture to ward / ordering physician.
References P.R. Murray, E.J. Baron, M.A. Pfaller, R.H. Yolken. 2003. Manual of Clinical Microbiology, 8th ed. ASM Press, Washington, D.C.

H.D. Izenberg. 2003. Respiratory Tract Cultures, – in Clinical Microbiology Procedures Handbook, 2nd ed. Vol.1 ASM Press, Washington, D.C.