Application Value of Metagenomics Next Generation Sequencing of Alveolar Lavage Fluid Metagenome in Unexplained Pulmonary Infection
Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200031, China
Baoqing Wang, Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200031, China, E-mail: Wang.firstname.lastname@example.org
To explore the application value of metagenomics next generation sequencing of alveolar lavage fluid metagenome in unexplained pulmonary infection. A total of 40 patients with pulmonary infection diagnosed in our hospital from January 2020 to December 2020 were collected. All patients underwent routine blood cell analysis, C-reactive protein, procalcitonin, 1,3-Beta-D glucan test, galactomannan test, sputum smear, sputum culture, blood culture+drug sensitivity, chest computed tomography and other examinations. In addition, sputum, broncho alveolar lavage fluid, blood, pleural effusion and other samples were collected to detect etiology and metagenomics next generation sequencing. Traditional laboratory methods detected pathogens in 60.00 % (24/40) samples, while metagenomics next generation sequencing detected pathogens in 87.50 % (35/40) samples. 12 cases were completely consistent with the traditional method; the results of 5 cases of metagenomics next generation sequencing were partially consistent with those of traditional methods. In these 5 cases, metagenomics next generation sequencing detected potential pathogens which were not detected by traditional methods; In 7 cases, the results of traditional methods were inconsistent with metagenomics next generation sequencing. Chlamydia psittaci was detected in 2 cases by metagenomics next generation sequencing. The results of etiological diagnosis showed that there was no difference in the positive rates of bacterial infection and fungal infection between metagenomics next generation sequencing and traditional methods (p>0.05). The positive rate of metagenomics next generation sequencing virus infection was 84.62 % (11/13), which was significantly higher than that of traditional methods 38.46 % (5/13) (p<0.05). In addition, 7 patients were diagnosed as atypical pathogen infection and the positive rate of metagenomics next generation sequencing was 100 % (7/7), which was significantly higher than that of traditional methods (14.29 %, 1/7) (p<0.05). For difficult and critical patients with infection, using metagenomics next generation sequencing to detect pathogens can improve the early detection rate of pathogens, achieve accurate and individualized treatment, shorten the length of hospital stay and reduce the mortality.