This study is being done because researchers want to learn more about genes that control the immune response in the participant's lungs and blood when the participant have lung disease leading to respiratory failure.

Primary Objective

To evaluate the feasibility of performing single cell gene expression analyses on tracheal aspirates from immunocompromised pediatric patients with immune compromising conditions, including HCT recipients.

Secondary Objectives

• To assess whether cell composition and activation states in longitudinally obtained tracheal aspirate and blood samples are able to distinguish unique immunopathology for each of the early post-HCT lung diseases.
• To assess whether cell composition and activation states in longitudinally obtained tracheal aspirate and blood samples are different between two immunodeficient patient populations (alloHCT vs non alloHCT) with lung disease and respiratory failure.
• To test the hypothesis that allogeneic T cell responses are implicated in the pathogenesis of early post-HCT lung diseases.

Exploratory Objectives

To correlate immune cell signaling in the lower respiratory tract and blood of patients with early post-HCT lung diseases with the presence or absence of pathogenic microbes at each site.

To explore HLA testing in Tracheal Aspirates in samples where enough cells are present.

This study involves a Tracheal aspirate, Bronchoalveolar lavage (BAL), and blood samples. The tracheal aspirates and blood samples will be obtained within 24 hours of intubation, then twice more every 3 -4 days, and then once a week until the patient is extubated. If the primary treatment team performs bronchoscopy with BAL, then an aliquot of residual BAL fluid will be obtained.

Inclusion Criteria:

• Participant is age 0 to 21 years old
• Participant has acute respiratory failure due to primary pulmonary disease and is expected to receive invasive mechanical ventilation for more than 48 hours

Exclusion Criteria:

• The primary etiology of respiratory failure is not related to primary pulmonary disease
• Aspiration is present
• The participant has a tracheostomy
• If the patient has undergone HCT, they are more than 100 days removed from HCT
• Has a diagnosis of severe combined immunodeficiency syndrome (SCIDS)
• The primary on-service team feels obtaining a study sample would be unsafe for any reason.
• Inability or unwillingness of research participant or legal guardian/representative to give written informed consent.

All participants who meet eligibility criteria and consent to enrollment on the study.