Although many researches have evaluated the performance of mNGS in different patients of different infection type(11, 17), there is still lack of studies on the utility of mNGS of BALF in immunocompromised hosts with pneumonia. In a multicenter prospective study of 329 severe community-acquired pneumonia (SCAP) patients, a higher detection rate (up to 90.3%) and an earlier detection for pathogens by mNGS of BALF than that of CMTs was reported(7). However, immunocompromised cases represented only less than 20% of the patients enrolled. Similarly, pan et al reported an improved detection for opportunistic pathogens by mNGS of BALF in 13 immunocompromised patients(5). On the contrary, peng et al showed a similar diagnostic performance of mNGS of BALF to CMTs for all types of pathogens in 60 immunocompromised patients(6). In this study, a higher microbial detection rate was showed in immunocompromised patients for using mNGS test of BALF than that of CMTs. For the diagnostic accuracy rate, there was no significant difference in bacteria and viruses’ infections by using these two methods. However, mNGS had a higher diagnostic accuracy than CMTs for fungal infections, which was not consistent with the study of Peng, mainly because of the low-proportion of aspergillus which was reported to be difficult for detection by mNGS test and high-proportion of pneumocystis in fungal infections in this study.
Pneumocystis jirovecii was the most common opportunistic pathogen in immunocompromised patients(18). It was reported to be responsible for 61.2% of confirmed pneumonia in immunocompromised patients (6) and 44.6% of SCAP in immunocompromised patients in a prospective study(7). Compare to CMTs, mNGS showed remarked advantages for detecting Pneumocystis jirovecii. Wang etc (19) showed significantly higher sensitivity of mNGS test than GMS alone for diagnosis PjP (100% vs. 30.7%). In the present study, the poor sensitivity of GMS for diagnosis PJP have be remarkably improved to 88% with the addition of serum BDG test. However, it was still lower than that of mNGS for diagnosis PJP. These results suggest that mNGS is a useful diagnostic tool with good performance for the diagnosis of PJP.
More polymicrobial infections were found in immunocompromised patients in comparison with immunocompetent patients(20). Peng etc(6) reported that more than half of microbiologically confirmed pneumonia having mixed infections. Pathogen detected by CMTs methods is usually a single one, while mNGS can detect multiple pathogens at the same time because of its unbiased detection technology, which has more advantages in the diagnosis of mixed infections(19, 21). In this study, 19 patients (37%) were identified as pulmonary polymicrobial infections. mNGS showed a higher detection rate and broader spectrum for pathogen detection than that of CMTs in mixed infection. Moreover, Pneumocystis jirovecii was found to be the most common pathogen in pulmonary mixed infection, which was similar to the previous study(22). Compare to CMTs, mNGS have identified much more co-pathogens of PJP. These results indicated that a remarkable advantage of mNGS method for identify mix pulmonary infection and detect co-pathogens of PJP than CMTs.
Rencently, an amount of cases of Chlamydia psittaci infection have been reported(23, 24). In our study, we have diagnosed 2 patients of Chlamydia psittaci infection solely by mNGS because of the lack of CMTs for Chlamydia psittaci and they were improved with a proper treatment. This result shows mNGS is also useful in the case of limited CMTs.
However, it was still a challenge for mNGS to identify Aspergillus or Cryptococcus because of the difficulty of DNA extraction from the thick polysaccharide cell wall(13, 25). In our study, the diagnosis sensitivity for IPA by CMTs is a litter higher than that of mNGS. As for cryptococcosis, the sensitivity arrived 100% by using CMTs, while only 1 case was identified by mNGS.
Our retrospective study contains certain limitations. Firstly, as a retrospective study, there were selection bias and recall bias which was inevitable. In addition, the lack of RNA sequencing and partial of PCR methods had failed to evaluate the diagnostic value of CMTs and mNGS better especially for virus infection. The interpretation of virus detected by mNGS was depended on the clinician's subjective judgment more than diagnostically confirmed. Finally, it was difficult to distinguish pathogens from colonization to infection due to the unbiased detection of mNGS without unified standard.