3. Results
Between July 2018 and July 2019, 12 male and 27 female patients with a median age of 38 years (15 to 77 years) were enrolled in the present study. 74% (29/39) patients were immune-impaired. 33 of the 39 patients were eventually diagnosed with lung infection, and 6 of the lung lesions were considered for non-infectious lesions. (9 cases) 23% of the cases were multiple infections. In the end, 43 infections were diagnosed in 33 patients with pulmonary infection, including 14 bacterial infections, 21 fungal pneumonia, 7 viral pneumonia and 1 mycoplasmal pneumonia. All of the patients in this study received empiric broad spectrum antibiotics prior to sample collection.
Performance of conventional culture for the identification of pathogens.
Cultures of BALF were positive in 7 of 43 pulmonary infections. Pathogenic microorganisms that were positive in culture of BALF include Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Corynebacterium and fungi. Pathogenic microorganisms detected only by mNGS, but not by culture, include Nocardia, Mycobacterium tuberculosis, Pneumocystis jirovecii, Haemophilus parainfluenzae, Streptococcus_pneumoniae, Pyramidobacter piscolens and Prevotella. The culture confirmed the bacterial pathogenic microorganisms in 2 out of 3 cases of P. aeruginosa pneumonia, 2 out of 2 cases of Klebsiella pneumoniae pneumonia, 1 case of E. coli pneumonia, and 1 case of Corynebacterium pneumonia. In one case, sputum smear showed positive acid-fast bacilli, mNGS detected Mycobacterium tuberculosis, and culture of BALF was negative. The sensitivity and specificity of microbial culture for diagnosis of pulmonary infection were 16.3% and 60.0%, respectively. The sensitivity of microbial culture for diagnosis of bacterial infections and fungal infections were 42.9% and 4.8%, respectively (Table 1). The positivity rates of mNGS and culture tests for bacterial infections, fungal infections, general infectious groups are illustrated in Figure 1. As expected, regardless of bacterial infections, fungal infections, or general infections, mGNS is more sensitive than conventional cultures.