Bronchoalveolar lavage fluid metagenomic next-generation sequencing assay for identifying pathogens in lung cancer patients

Background: For patients with lung cancer, timely identification of new lung lesions as infectious or noninfectious, and accurate identification of pathogens is very important in improving OS of patients. As a new auxiliary examination, metagenomic next -generation sequencing (mNGS) is believed to be more accurate in diagnosing infectious diseases in patients without underlying diseases, compared with conventional microbial tests (CMTs). We designed this study to find out whether mNGS has better performance in distinguishing infectious and non-infectious diseases in lung cancer patients using bronchoalveolar lavage fluid (BALF). Materials and Methods: This study was a real -world retrospective review based on electronic medical records of lung cancer patients with bronchoalveolar lavage (BAL) and BALF commercial mNGS testing as part of clinical care from 1 April 2019 through 30 April 2022 at The First Affiliated Hospital of Sun Yat-sen University. 164 patients were included in this study. Patients were categorized into the pulmonary non-infectious disease (PNID) group (n = 64) and the pulmonary infectious disease (PID) group (n = 100) groups based on final diagnoses. Results: BALF mNGS increased the sensitivity rate by 60% compared to CMTs (81% vs. 21%, p < 0.05), whereas there was no significant difference in specificity (75% vs. 98.4%, p > 0.1). Among the patients with PID, bacteria were the most common cause of infection. Fungal infections occurred in 32% of patients, and Pneumocystis Yersini was most common. Patients with Tyrosine kinase inhibitors (TKIs) therapy possess longer overall survival (OS) than other anti-cancer agents, the difference between TKIs and immunocheckpoint inhibitors (ICIs) was insignificant (median OS TKIs vs. ICIs vs. Anti-angiogenic vs. Chemo vs. Radiotherapy = 76 vs. 84 vs. 61 vs. 58 vs. 60). Conclusions: our study indicates that BALF mNGS can add value by improving overall sensitivity in lung cancer patients with potential pulmonary infection, and was outstanding in identifying Pneumocystis infection. It could be able to help physicians adjust the follow-up treatment to avoid the abuse of antibiotics.