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).