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Patients with neutropenia (an abnormally low level of neutrophils) are at a high risk for life-threatening bacterial and/or fungal infections after high-dose chemotherapy for acute leukemia (AL) and allogenic stem cell transplant (SCT). Identification of these invasive microbes currently relies on enzymatic or culture-dependent methods, which have limited sensitivity and specificity.

The project employed a deep amplicon sequencing metagenomic strategy to better define the microbial populations in bronchoalveolar lavage samples from these patients. The team assessed microbial diversity showing an overall decrease in microbial diversity and abundance in the immunocompromised patients, compared to healthy controls.

Overall, this work has expanded the knowledge of the diversity of respiratory tract microbial communities in both healthy and immunocompromised patients. This is informative regarding the potential utility of these methods as clinical assays for identifying microbial pathogens in AL and SCT patients with lung infections of unknown origin.