Clinical decision making impact of Next-Generation Sequencing in Pneumocystis jirovecii infection: infection characteristics and prognosis.

PURPOSE: While next-generation sequencing (NGS) enables detection of Pneumocystis jirovecii and other invasive fungi, its clinical utility remains largely unexplored beyond methodological validation studies.

METHOD: We retrospectively analyzed clinical characteristics and disease progression in patients with NGS-positive P. jirovecii infections identified between March and August 2024.

RESULTS

In our cohort of 37 patients, males showed higher P. jirovecii detection rates than females. Patients aged ≥60 years presented more severe pneumonia symptoms, including fever, cough, sputum production, dyspnea, and lung rales. Clinical assessment and NGS results stratified patients into diagnosed (n = 31) and excluded (n = 6) groups. The diagnosed group exhibited significantly higher NGS reads, neutrophil-lymphocyte ratio, LDH, and 1,3-β-d-glucan levels (P < 0.05), while showing lower albumin and lymphocyte ratios (P < 0.05). Radiologically, the diagnosed group demonstrated universal ground-glass opacities (100 %), with frequent pleural effusion (35.48 %) and mediastinal lymphadenopathy (54.84 %). These patients commonly presented co-infections and co-colonization with Klebsiella pneumoniae, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV). NGS-guided therapeutic intervention led to successful treatment in 83.9 % (26/31) of diagnosed cases, while 16.1 % (5/31) showed poor outcomes due to delayed diagnosis and treatment failure.

CONCLUSION

NGS detection of P. jirovecii enables accurate diagnosis and guides therapeutic interventions, leading to improved clinical outcomes. In clinical decision-making, compared with fungal staining or quantitative polymerase chain reaction (qPCR), these findings establish NGS as a valuable tool in diagnostic and treatment algorithms for P. jirovecii infections.