Figure legends
Fig. 1 Positivity rate comparison between metagenomic next-generation sequencing (mNGS) and microbial culture for bacterial infections (n = 14), fungal infections (n = 21), general infectious (n = 43). The number of positive samples (y-axis) for mNGS is plotted against the mNGS and microbial culture for bacterial infections (n = 14), fungal infections (n = 21), general infectious groups (x-axis).
Fig.2 Positivity rate comparison between metagenomic next-generation sequencing (mNGS) of transbronchial lung biopsy (TBLB), bronchoalveolar lavage fluid (BALF) and bronchial needle brushing (BB) samples, and mNGS of TBLB + BALF + BB for bacterial infections (n = 14), fungal infections (n = 21), general infectious (n = 43). The number of positive samples (y-axis) for mNGS is plotted against the TBLB, BALF, BB and TBLB + BALF + BB groups (x-axis).
Fig. 3 A: typical septate hyphae with sharp-angled bifurcation could be found with rapid on-site cytological evaluation (ROSE), the red arrow refers to sharp-angled bifurcation, and the green arrow refers to the septate of the hyphae. (Diff-Quik [DQ] stain, 1000 × magnification); B ~ D: Cryptococcus was detected by ROSE in three patients, the blue arrow refers to Cryptococcus (DQ stain, 1000 × magnification).
Fig. 4 Comparison of relative abundance of bacterial pathogens, fungal pathogens and viral pathogens in patients with bacterial (A), fungal (B) and viral (C) infections, respectively against the three types of specimens (transbronchial lung biopsy (TBLB), bronchoalveolar lavage fluid (BALF) and bronchial needle brushing (BB) specimens).
Fig. 5 Comparison of relative abundance of Prevotella (A), Neisseria (B), Veillonella (C), Streptococcus (D), Fusobacterium (e) and Rothia (F) in all of the researched objects against the three types of specimens (transbronchial lung biopsy (TBLB), bronchoalveolar lavage fluid (BALF) and bronchial needle brushing (BB) specimens).
Fig. 6 common oropharyngeal microbiota richness in TBLB, BALF and BB specimens.