Metagenomic Assessment of the Pathogenic Risk of Microorganisms in Sputum of Postoperative Patients With Pulmonary Infection

被引:8
作者
Chen, Junji [1 ]
Sun, Lianjie [2 ]
Liu, Xiaoying [1 ]
Yu, Qixiang [1 ]
Qin, Kaijie [1 ]
Cao, Xuejie [2 ]
Gu, Jianwei [1 ]
机构
[1] Shanghai Jiao Tong Univ, Ruijin Hosp, Dept Cardiovasc Surg, Sch Med, Shanghai, Peoples R China
[2] Genoxor Med Sci & Technol Inc, Ningbo, Zhejiang, Peoples R China
基金
中国国家自然科学基金;
关键词
pulmonary infection; sputum microbiome; metagenomic next-generation sequencing; pathogen risk; limit of detection; opportunistic pathogen; strain profiling; CANDIDA-ALBICANS; MICROBIOME; ALIGNMENT; COLONIZATION; TRANSMISSION; DIVERSITY; BACTERIA; AGENTS; SCORE; TOOL;
D O I
10.3389/fcimb.2022.855839
中图分类号
R392 [医学免疫学]; Q939.91 [免疫学];
学科分类号
100102 ;
摘要
Respiratory infections are complicated biological processes associated with an unbalanced microbial community and a wide range of pathogens. To date, robust approaches are still required for distinguishing the pathogenic microorganisms from the colonizing ones in the clinical specimens with complex infection. In this study, we retrospectively analyzed the data of conventional culture testing and metagenomic next-generation sequencing (mNGS) of the sputum samples collected from 50 pulmonary infected patients after cardiac surgery from December 2020 and June 2021 in Ruijin Hospital. Taxonomic classification of the sputum metagenomes showed that the numbers of species belonging to bacteria, fungi, and viruses were 682, 58, and 21, respectively. The full spectrum of microorganisms present in the sputum microbiome covered all the species identified by culture, including 12 bacterial species and two fungal species. Based on species-level microbiome profiling, a reference catalog of microbial abundance detection limits was constructed to assess the pathogenic risks of individual microorganisms in the specimens. The proposed screening procedure detected 64 bacterial pathogens, 10 fungal pathogens, and three viruses. In particular, certain opportunistic pathogenic strains can be distinguished from the colonizing ones in the individual specimens. Strain-level identification and phylogenetic analysis were further performed to decipher molecular epidemiological characteristics of four opportunistic etiologic agents, including Klebsiella pneumoniae, Corynebacterium striatum, Staphylococcus aureus, and Candida albicans. Our findings provide a novel metagenomic insight into precision diagnosis for clinically relevant microbes, especially for opportunistic pathogens in the clinical setting.
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页数:11
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