Assessing Nanopore Targeted Sequencing for the Diagnosis of Pulmonary Infections: A Comparative Multidisease Approach

Pulmonary infections remain a significant global health burden, particularly in immunocompromised individuals and patients with chronic respiratory or systemic diseases. Conventional microbiological tests (CMTs), though widely used, often have limited sensitivity and delayed results, especially in polymicrobial or atypical infections. This study evaluated the diagnostic performance of nanopore targeted sequencing (NTS) in 284 patients with suspected lower respiratory tract infections at Chifeng Municipal Hospital, using CMTs and clinical diagnosis as references. NTS demonstrated markedly higher sensitivity (91.85%) compared to CMTs (74.81%), with substantial improvements in detecting fungal (81.7%) and mixed infections (99.65%). A total of 259 pathogens were detected. Among them, bacteria were the most frequently identified pathogens (69.5%), followed by fungi (15.44%) and viruses (14.28%). Pathogen distribution varied by clinical subgroup, such as community-acquired pneumonia and chronic obstructive pulmonary disease, reflecting infection heterogeneity. Patients with hypertension (HBP) showed a higher incidence of fungal and mixed infections than non-HBP patients. NTS was particularly effective in detecting opportunistic pathogens in the HBP group, suggesting an association between cardiovascular comorbidity and altered pathogen susceptibility.