Next-Generation Sequencing in Immunocompromised Hosts with Pulmonary Infections: A Prospective Diagnostic Study from Northern India

Background: Immunocompromised hosts (ICH) with pulmonary infections frequently present diagnostic challenges, as conventional microbiological tests offer low sensitivity, especially in patients with prior antimicrobial exposure. This study investigates the diagnostic utility and clinical impact of next-generation sequencing (NGS) in such patients. Methods: In a prospective cohort study conducted from May 2023 to January 2025 at CSSH, Meerut, we enrolled 65 immunocompromised patients presenting with bilateral pulmonary infiltrates and symptoms of lower respiratory infection. All patients underwent conventional culture and NGS testing. Diagnostic yields, concordance, and clinical impact were evaluated, and the diagnostic performance of NGS was compared to culture using kappa statistics and standard metrics. Results: The majority were male (75.4%), with the most common age group being >60 years (33.85%). Hematologic malignancies (41.54%) and diabetes mellitus (32.31%) were the leading causes of immunosuppression. Radiographic abnormalities were present in all patients; cough (60%), sputum production (30.77%), dyspnea (33.85%), and fever (26.15%) were the predominant symptoms. Culture detected pathogens in 41.54% of cases, while NGS identified pathogens in 50.77%. Concordance between methods was high (κ = 0.78, p = 0.007). NGS demonstrated higher sensitivity (72.73%) and specificity (90.62%) with an accuracy of 81.54%. NGS identified more bacterial (n=31 vs 19) and viral (n=12 vs 2) pathogens than culture, which favored fungi (n=26 vs 13). Clinically, NGS supported a definitive diagnosis or ruled out active infection in 18.46% and 10.77% of cases, respectively. Conclusions: NGS improves diagnostic yield and informs clinical decision-making in ICH with pneumonia, particularly in culture-negative or polymicrobial cases. Its integration into clinical workflows can refine antimicrobial stewardship and optimize outcomes.