The performance of mNGS and standard procedures for detecting Cryptococcus
mNGS seemed to be inferior to serum antigen testing for detecting Cryptococcus. Serum cryptococcal capsular polysaccharide antigen was positive for all of patients with Cyptococcal pneumonia, while one case was missed and unidentifiable by mNGS. ROSE showed granulomatous inflammation in all cases. Cryptococcus was detected by ROSE in three of these four patients (Fig. 3B ~ D, Table 3).
Characteristics of pathogens and common oropharyngeal microbiota in different types of specimens.
Figure 4 and Table 4 show the comparison of the relative abundance of pathogenic microorganisms (which refers to the ratio of the number of reads of pathogenic microorganisms detected to the number of reads of the same type of microorganism detected throughout the samples.) at the species level with mNGS obtained from TBLB, BALF and BB samples. The statistical analysis showed that the relative abundance of pathogenic bacteria (Fig. 4A), pathogenic fungi (Fig. 4B) and pathogenic viruses (Fig. 4C) was not statistically different among the three specimens.
We compared six kinds of common oropharyngeal microbiota (Prevotella, Neisseria, Streptococcus, Veillonella, Fusobacterium, and Rothia) richness (which refers to total number of different genera out of the six genera identified in each sample) and the relative abundance at the genus level against the three types of samples (TBLB, BALF and BB samples). Surprisingly, we found no statistically significant differences between TBLB and BB specimens with respect to abundanceof all of these six kinds of common oropharyngeal microbiota (Table 5 and Fig.5). The relative abundance of Prevotella in BALF specimens was higher than that of TBLB specimens and the relative abundance of Veillonella in BALF specimens was higher than that of BB specimens (Table 5 and Fig5). The total number of different genera in TBLB, BALF and BB specimens was 2.90 [2.39 ~ 3.41], 4.28 [3.79 ~ 4.78] and 4.13 [3.56 ~ 4.70], respectively. Community richness in the TBLB specimens significantly decreased than that of BALF specimens and BB specimens. (Fig. 6).