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Compared with conventional diagnostic methods, metagenomic sequencing is better in detecting novel, rare, and unexpected pathogens and being applied in co\u2010infections. Meanwhile, it can also provide more comprehensive information about pathogens. However, metagenomic sequencing still has limitations. Also, the situations that should be applied in and how the results should be interpreted are discussed in this review.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Metagenomic sequencing improves efficiency to identify pathogens compared with traditional diagnostic methods and can be applied in clinical diagnosis. However, the technology of metagenomic sequencing still needs to be improved. Also, clinicians should learn more about when to use metagenomic sequencing and how to interpret its results.<\/jats:p><\/jats:sec>","DOI":"10.1111\/crj.13538","type":"journal-article","created":{"date-parts":[[2022,9,7]],"date-time":"2022-09-07T04:38:20Z","timestamp":1662525500000},"page":"646-656","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":74,"title":["Advantages and challenges of metagenomic sequencing for the diagnosis of pulmonary infectious diseases"],"prefix":"10.1111","volume":"16","author":[{"given":"Yan","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Institute of Respiratory Medicine Tongji University School of Medicine  Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li\u2010Chao","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care 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