Our study retrospectively evaluated the value of mNGS in peripheral pulmonary infection by performing mNGS and traditional pathogen detection in specimens obtained by bronchoscopy. Most of the patients enrolled in this study had hematologic malignancy or autoimmune deficiency disease. These patients were chronically immunocompromised due to long-term use of large doses of antitumor drugs, cytotoxic drugs, or glucocorticoids, and were prone to complicating diseases, especially pulmonary complications[5–6].
When pulmonary lesions occur, the lesions should be judged quickly and accurately to guide the proper follow-up treatment. Since the clinical manifestations of some infectious diseases and non-infectious diseases are very similar, this is more difficult to distinguish by routine laboratory examination and imaging analysis, where there are often overlap characteristics between diseases. This present study revealed that mNGS has obvious differential significance between pulmonary infection and non-pulmonary infection, and the detection rate of pathogens in pulmonary infection is significantly higher than that in non-pulmonary infection, and accompanied by a higher microbial sequencing reads. Moreover, mNGS was able to identify nearly 71.4% of patients with pulmonary infection, which was higher than traditional pathogen detection, at 17.9% (P < 0.001), and the median detection time is shorter(48.5 hours vs 72 hours). We speculated that the reason may be the effect of the use of antimicrobials on bacterial culture among the bacteria with negative bacterial culture but positive by mNGS. Because mNGS was to directly extract all nucleic acid fragments from samples and detect them. The use of antibiotics had no obvious effect on the detection results, which was one of the advantages of mNGS.
At present, the most common pathogen detection methods in specimens are microbial culture, histopathology and smear microscopic examination. The microbial culture in tracheoscopes included tissue culture and BALF culture[7–8], but the sensitivity was low, and the positive rate was related to many factors, histopathology and smear microscopic examination could only identify a limited number of fungal species or Mycobacterium tuberculosis. For virus detection, the above test methods are not applicable[9–12]. In our study, interventional specimens were obtained from patients with suspected pulmonary infection by bronchoscopy and sent for mNGS analysis. In addition, mNGS was more specific and sensitive, with a specificity of 100% and a sensitivity of 90.9%, while the specificity of traditional methods was only 83.3% and 18.2% (P < 0.001), which may be due to the traditional methods were unable to detect more microorganisms, resulting in a higher true negative rate of non-pulmonary infections[13–18]. Above of all, the AUC of mNGS was 95.45%, while the AUC of traditional pathogen detection was 50.76%, which indicated that mNGS may play an important role in the diagnosis of peripheral pulmonary infectious lesions among children.
Interestingly, we found that decreased WBC counts were associated with the presence of microbial DNA, and was inversely proportional to the number of sequencing reads, which was consistent with previous reports[19–20]. It’s known to all, neutropenia often occurs in pediatric patients with malignant hematology after chemotherapy, resulting in severe infection. This result also suggested that we should increase the counts of WBC in time during the interval of chemotherapy, which plays a significant role in reducing the infection rate. On the other hand, we also discovered that when CRP is less than 60mg/dl, CRP increases with the increase of microbial sequencing reads, which suggested that CRP can be used as an index to detect the curative effect of anti-infection.
The study has several limitations. Most importantly, it is a single centre retrospective study, so bias in this study was inevitably. Secondly, the sample size of this research was still small. In spite of these limitations, this study does provide a new perspective for studying the value of alveolar lavage fluid metagenomic next-generation sequencing in the diagnosis of peripheral pulmonary infectious lesions among children.