ETIOLOGICAL DIAGNOSTIC VALUE OF TARGETED NEXT-GENERATION SEQUENCING FOR PNEUMONIA

Abstract

 Pneumonia is a common respiratory infection and a significant contributor to global mortality.  Prompt identification of the pathogens responsible for pneumonia is crucial for ensuring effective treatment of patients.  The study assessed the efficacy of targeted next-generation sequencing (tNGS) using bronchoalveolar lavage fluid samples from pneumonia patients (n = 338).  The tNGS assay identified 70 pathogens, including 38 bacteria species, 14 types of viruses, 13 fungi species, 2 Mycoplasma spp, Ureaplasma urealyticum, Ureaplasma parvum, and Chlamydia.  Among infections with a single pathogen, Candida albicans (12%) and Mycobacterium tuberculosis complex (11%) were the most common pathogens, while the fungi/viruses combination was predominant (28%) in cases of infection with multiple pathogens.  Notably, tNGS method had a significantly higher positive detection rate (90%; 95% confidence interval (CI) of 86 to 93%) and higher coincidence rate (92%; 95% CI of 89 to 95%) compared to the conventional method (33%; 95% CI of 28 to 38%) and 82%; 95% CI of 76 to 85%) with p-values <0.001 and 0.008 respectively), particularly in identifying M. tuberculosis and atypical pathogens (C. psittaci, Chlamydia pneumoniae, Coxiella burnetii, Legionella spp, and Mycoplasma pneumoniae).  Treatment in 50% of the cases was based solely on tNGS results.  We conclude that tNGS is an important diagnostic tool in treating pulmonary infection, owing to its high sensitivity, specificity and rapidity in detecting causal pathogenic bacteria, atypical organisms, fungi and viruses, allowing targeted drug treatment irrespective of prior empirical medication, thereby potentially improving patients’ clinical outcomes and survival.