Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers

by Zareen Fatima, Matthew D. Surette, Sarah Marttala, Daniela Leto, Padman Jayaratne, Fiona Smaill, Marek Smieja, Mohammad Rubayet Hasan Background Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time.

While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.

Methods BAL specimens from healthy control volunteers (n = 20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n = 52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology.