Several issues in interpreting the results of metagenomic next generation sequencing of lower respiratory tract infection

Abstract

Metagenome next generation sequencing (mNGS) is an important method for pathogen diagnosis of lower respiratory tract infection, but there are many difficulties in interpreting mNGS reports. The Expert Consensus on Clinical Interpretation Path of mNGS of Lower Respiratory Tract Infection, completed by Chinese Thoracic Society, provides a detailed path and guidance for report interpretation. The expert consensus covers clinical medicine, microbiology, molecular diagnosis and other aspects. On this basis, several important clinical issues need to be highlighted. First, the lower respiratory tract specimens used for mNGS must be obtained in a timely and qualified manner. Second, the correct interpretation of the mNGS report needs to be based on a full understanding of the patients and their conditions. Third, the quality of the report should be analyzed according to the main parameters in the mNGS report. Fourth, an understanding of basic microbiology knowledge is beneficial to identify valuable pathogens in the mNGS report. Fifth, other microbiological methods should be actively used during mNGS detection. Sixth, to seek the help of the team when necessary and organize multidisciplinary discussions are vital. Seventh, it is important to constantly adjust the diagnosis and treatment strategies according to the clinical treatment response to treatment and the evolution of the disease. In a word, the interpretation of mNGS results needs to refer to specimen types and sequencing parameters, to combine with the specific conditions of patients in detail, to collect a variety of microbiological test results, to carefully screen and make judgement according to the treatment effect and disease outcome, and finally to make the diagnosis. The interpretation of mNGS report also requires us to have more knowledge of microbiology, sequencing and bioinformatics analysis, and to pay more attention to the strength of the team to discriminate the truth in multidisciplinary collaboration.