Specimen Submission Guidelines for Pathologic Evaluation of Suspect Pneumonia Infections

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Respiratory tract infections and pneumonias can be caused by a variety of bacteria, viruses, fungi and other microorganisms. Histopathologic changes in tissues and the distribution of microbial pathogens can vary significantly among different pneumonias. Microbial pathogens may be sparsely distributed in tissues and/or may preferentially involve airways or pulmonary parenchyma; as a result, collection and submission of the appropriate tissues ensures the best chance of detecting the pathogen. Performance of specific immunohistochemical, molecular, or other assays will be determined based on clinical and epidemiologic information provided by the submitter and the histopathologic features identified in the submitted tissue specimens.

Collection of Tissue Specimens

The preferred specimens would be a minimum of 8 blocks and fixed tissue representing the different pulmonary sites listed below. In addition, specimens from other organs showing significant pathology should be submitted. Formalin-fixed, paraffin-embedded blocks made from BAL can also be submitted when available. The preferred pulmonary sites include:

  1. Hilar lung with segmental bronchi, primary bronchi
  2. Trachea, upper and lower
  3. Peripheral pulmonary parenchyma from both lungs

Specimens should be included from any other organ showing significant gross or microscopic pathology.

Submission of Specimens

Paraffin-embedded tissue blocks

In general, this is the preferred specimen and is especially important to submit in cases where tissues have been in formalin for a significant time. Prolonged fixation (>2 weeks) may interfere with some immunohistochemical and molecular diagnostic assays.

Wet tissue

If available, we highly recommend that unprocessed tissues in 10% neutral buffered formalin be submitted in addition to paraffin blocks. The volume of formalin used to fix tissues should be 10x the volume of tissue. Place tissue collected according to the dimensions provided above in 10% buffered formalin for three days (72 hours) for biopsies, and a week for thinly-sliced autopsy tissues. After fixation, if not paraffin-embedded, tissues SHOULD be transferred to 70% ethanol for long term storage and for shipping.

Electron Microscopy (EM) specimens

Samples should be fixed in glutaraldehyde and held in phosphate buffer. Sample containers are filled to the top with phosphate buffer and sent on wet ice.  Do not freeze.  Epoxy-embedded tissues are also accepted.

Please refer to our General Guidelines for Submitting Pathology Specimens.