Next-generation Sequencing Of The BALF In The Diagnosis Of Severe Pneumonia In Patients With Autoimmune Diseases

Background:Autoimmune diseases are one of the serious challenges in clinical practice.This retrospective study aimed to examine whether next-generation sequencing(NGS)can be used to identify causative pathogens of bronchoalveolar lavage fluid(BALF)in severe pneumonia,compared to the standard procedures.Methods:This retrospective study included patients with autoimmune diseases accompanying severe pneumonia,and admitted at the intensive care unit(ICU)of BinJiang campus of The Second Affiliated Hospital of Zhejiang University School of Medicine,and accepted fiberoptic bronchoscopy to get the BALF samples to help found the causative pathogens between December 2017 to February 2019.The BALF specimens were divided into two equal parts,One was sent for standard procedures.Another one was sent for mNGS.For analysis of causative pathogens by mNGS compared to standard procedures.Results:18 BALF samples collected from the 17 enrolled patients(7 men;mean age 55 years),a total of 15 samples(83.3%)were mNGS-positive.6 samples(33.3%)were standard procedures-positive.The 6 standard procedures-positive samples were also mNGS-positive,5 of which were consistently identified as abnormal values by mNGS,only one conflicts between mNGS and standard procedures.Almost all the virus and Pneumocystis jiroveci were obtained only in mNGS.Six bacteria,one virus and one fungus were detected in the standard procedures,mNGS identified eleven species of bacteria,one chlamydia,four fungi and six viruses.Compared with standard procedures,mNGS showed a significantly higher positive rate in detecting pathogen(33.3%vs 83.3%,p=0.006),mNGS especially showed a significantly higher positive rate in detecting virus(5.6%vs 38.9%,p=0.041),fungus(11.1%vs 50.0%,p=0.027).but no significant difference in detecting pathogenic bacteria(27.8%vs50.0%,p=0.305).Conclusion:For severe pneumonia with autoimmune diseases,mNGS has unique advantages in the identification of chlamydia,fungus and virus in this population.