Abstract
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.
Highlights
As is well known, postoperative pulmonary infections are characterized by cough, phlegm, shortness of breath, chest pain, and temperature above 38 degrees (Conde and Lawrence, 2008)
The samples were subject to conventional culture and metagenomic next-generation sequencing (mNGS) testing for species
To assess the pathogenic risk of individual microorganisms, we proposed the abundance limits of detection (LOD) for screening candidate pathogens based on mNGS assays and species-level abundance profiles of bacteria, fungi, and viruses, respectively (Table S3)
Summary
Postoperative pulmonary infections are characterized by cough, phlegm, shortness of breath, chest pain, and temperature above 38 degrees (Conde and Lawrence, 2008). The etiological agents causing respiratory tract infections (RTIs) are usually related to a wide variety of pathogenic microbes (Cappelletty, 1998; Chowdhary et al, 2016; Kutter et al, 2018). A study on 426 patients with suspected lower RTIs has revealed that the most prevalent bacterial species isolated from the specimens (i.e. sputum, endotracheal secretion, and bronchial washing) were. Several studies on respiratory infections have reported that. Schizophyllum commune belonging to filamentous basidiomycetes is an emerging fungal pathogen, and its culture and species identification need a couple of weeks under specific culture media (Chowdhary et al, 2013; Chowdhary et al, 2016). Many members of the human respiratory tract microbiota are colonizing opportunistic pathogens that are normally harmless and, when the microbial homeostasis becomes disrupted, can cause infections (Price et al, 2017)
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